Congratulations guys, this thread made me think and register so I could share what I thought up.
At first I was thinking about grouping powers by source, but then I realized that the system I was building in my head would allow the creation of a wizard with the toughness of a fighter. I also realized that power source actually doesn't do anything at all, but party roles (controller, defender, leader, striker) are crucial to 4th edition gameplay. I followed this trail of though and the final result is written below. It's a fairly long post, but that's what can be expected of 5 hours worth of reading, thinking and writing.
You start by picking a party role: defender, leader, striker. I didn't list controller because there is only 1 controller class in the PHB1 so you don't really have anything to mix with in the first place. Anyway, the role you selected determines basic hit points (15 for defenders, 12 for leaders and strikers), the hit points gained per level (6 for defenders, 5 for leaders and strikers), as well as number of healing surges per day (9 for defenders, 7 for leaders, 6 for strikers). Constitution score and modifier apply as normal.
Second you select your weapon and armor proficiencies. The number of proficiencies you pick depends on the role you selected (defender selects 11, leader selects 7, striker selects 5), but all classes start out proficient with cloth armor and two simple melee weapons of the player's choice. In addition players can choose from the following:
ARMOR
-leather armor proficiency
-hide armor proficiency (requires leather armor proficiency)
-chainmail proficiency (requires hide armor proficiency)
-scale armor proficiency (requires chainmail proficiency)
-plate armor proficiency (requires scale armor proficiency)
-light shield proficiency
-heavy shield proficiency (requires light shield proficiency)
WEAPONS
-proficiency with all simple melee weapons
-proficiency with 1 military melee weapon (requires proficiency with a simple melee weapon from the same category - heavy blades, axes, etc.)
-proficiency with all military melee weapons (requires proficiency with all simple melee weapons)
-proficiency with 1 superior melee weapon (requires proficiency with a military melee weapon from the same category - heavy blades, axes, etc.)
-proficiency with all simple ranged weapons
-proficiency with all military ranged weapons (requires proficiency with all simple ranged weapons)
-proficiency with shurikens (requires proficiency with daggers)
IMPLEMENTS
-proficiency with holy symbols (only works for divine powers; a Holy Avenger weapon counts as a holy symbol for paladin powers)
-proficiency with rods and wands (only works for warlock powers)
-proficiency with Pact Blades as implements (only works for warlock powers, requires proficiency with rods and wands)
You can also sacrifice a number of proficiencies to gain an equal amount of bonus feats. The exact number is up to the DM, but as a general rule 3 ought to be enough (we don't want to exaggerate).
Next you have 2 points to spend on defense bonuses (fortitude, reflex, will). You can get a +1 bonus on two different defenses or give a +2 bonus to a single defense.
After that you select starting skills. Defenders select 4 skills from the combined skill lists of all defender classes (until so far that means fighter and paladin), leaders select 4 skills from the combined skill lists of all leader classes (cleric and warlord), and strikers select 5 skills from the combined skill lists of all striker classes (ranger, rogue, warlock). Skill selection is important because you need to be trained in Religion and worship a deity to use divine powers and select class features from divine classes (paladin, cleric), trained in Arcana to use arcane powers and select features from arcane classes (warlock), and trained in a physical skill to use martial powers and select features from martial classes (fighter, ranger, rogue). Physical skills are the skills that can get a check penalty from wearing certain armor (Acrobatics, Athletics, Endurance, Stealth, Thievery).
The fifth step is selecting class features. Defenders select 3 class features from all defender classes. They must take one and only one feature that allows them to mark enemies (because marking is what makes them defenders, but we don't want them to be overpowered). With the PHB1 you can choose between the paladin's Divine Challenge and the fighter's Combat Challenge. The other features from which you can choose are Combat Superiority, Fighter Weapon Talent, Lay on Hands, and Channel Divinity (both Divine Mettle and Divine Strength). In order to allow the system to perfectly recreate the paladin as presented in the PHB Lay on Hands comes with 1 bonus healing surge and +1 to one defence (fortitude, reflex, will). As mentioned before you need to be trained in Religion and worship a deity to select the paladin's features and trained in a physical skill to select the fighter's features.
Leaders select 3 features from all leader classes. They must take one and only one feature that allows them to heal (because healing is what makes them leaders, but we don't want them to be overpowered). With the PHB1 you can choose between the cleric's Healing Word and the warlord's Inspiring Word. The effects of the two are identical, but with this custom class system they determine your class for purpose of selecting feats and paragon paths so choose accordingly. The other features from which you can choose are Channel Divinity (both Divine Fortune and Turn Undead), Healer's Lore, Combat Leader, and Commanding Presence (select either Inspiring Presence or Tactical Presence but not both). As mentioned before you need to be trained in Religion and worship a deity to select the cleric's features and trained in a physical skill to select the warlord's features.
Strikers select 4 features from all striker classes. They must take one and only one feature that allows them to inflict additional damage (because damage is what makes them strikers, but we don't want them to be overpowered). With the PHB1 you can choose between the ranger's Hunter's Quarry, the rogue's Sneak Attack, and the warlock's Warlock's Curse. The other features from which you can choose are Fighting Style (either Archer fighting Style or Two-Blade Fighting Style but not both), Prime Shot, First Strike, Rogue Tactics, Rogue Weapon Talent (requires proficiency with daggers and shurikens), Eldritch Pact (select 1 of the 3; requires Warlock's Curse class feature), and Shadow Walk. As mentioned before you need to be trained in a physical skill to select the ranger's and rogue's features and trained in Arcana to select the warlock's features. Since Prime Shot is a class feature for both the ranger and the warlock you can select it if you are trained either in Arcana or any physical skill.
Regardless of which role you wish your class to perform you can also trade a feature for an additional armor/weapon/implement proficiency.
Finally you also get to pick powers. At level 1 you select 2 at-will powers (3 if you are Human), 1 encounter power, and 1 daily power from all classes that match your role. So (with PHB1) defenders pick fighter and paladin powers, leaders pick cleric and warlord powers, and strikers pick, ranger, rogue and warlock powers. If you took the Eldritch Pact feature you do not have to pick the pact's at-will power unless your DM insists on it. At level 2 you again pick 1 utility power from any class that matches your role. However, at higher classes you can pick powers from all classes. The limitation is that if you pick a power from a class that does not match your role, it must be of lower level. For example a level 3 defender can pick any level 3 fighter or paladin power, or he can pick a level 1 daily power from another class. A further limitation is that again you need to be trained in Religion to use divine powers, trained in Arcana to use arcane ones, and trained in a physical skill to use martial ones.
This last rule can be used to spice up wizards as well. Whenever your wizard learns a new encounter/daily/utility spells he can instead gain an encounter/daily/utility power of lower level from another class. Note however, that while a wizard normally learns 2 daily/utility spells when he levels up you can only select 1 power from another class. A further limitation is that yet again you need to be trained in Religion to use divine powers and trained in a physical skill to use martial ones.
For the purpose of selecting feats (including multiclass feats) and paragon paths you are considered to be a ...
- cleric if you have the Healing Word class feature
- fighter if you have the Combat Challenge class feature
- paladin if you have the Divine Challenge class feature
- ranger if you have the Hunter's Quarry class feature
- rogue if you have the Sneak Attack class feature
- warlock if you have the Eldritch Pact class feature
- warlord if you have the Inspiring Word class feature
Note: if you wish to use cleric, paladin and warlock powers and pursue the paragon paths of these classes it is highly recommended to also be proficient with the appropriate implements, even though they are not listed as a requirement. Also, it is possible to not match any of the above requirements if you select Warlock's Curse without also selecting Eldritch Pact. This is a little tricky and would best be avoided.
Speaking of feats, here are 3 new heroic tier ones designed specifically for this system:
DEFENDER
Requirement: you are not already a defender; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them from defender classes (fighter and paladin). However, you still cannot select Combat Challenge and Divine Challenge class features. You also still need to be trained in the relevant skill.
LEADER
Requirement: you are not already a leader; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them from leader classes (cleric and warlord). However, you still cannot select Healing Word and Inspiring class features. You also still need to be trained in the relevant skill.
STRIKER
Requirement: you are not already a striker; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them from striker classes (ranger, rogue, warlock). However, you still cannot select any out of Hunter's Quarry, Sneak Attack, and Warlock's Curse. You also still need to be trained in the relevant skill.
However, if there are 3 or less players the DM might change the feats like this (changes are in capitals):
DEFENDER
Requirement: you are not already a defender; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them powers from defender classes (fighter and paladin). However, you cannot select BOTH Combat Challenge and Divine Challenge class features. You also still need to be trained in the relevant skill.
LEADER
Requirement: you are not already a leader; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them from leader classes (cleric and warlord). However, you cannot select BOTH Healing Word and Inspiring class features. You also still need to be trained in the relevant skill.
STRIKER
Requirement: you are not already a striker; you can only take this feat at level 1
Effect: When selecting class skills, features, and level 1 and 2 powers you can select them from striker classes (ranger, rogue, warlock). However, you cannot select MORE THAN ONE out of Hunter's Quarry, Sneak Attack, and Warlock's Curse. You also still need to be trained in the relevant skill.
This way the present players can take over the crucial ability of the missing party role.
You can also use these feats to replace a wizard class feature with a class feature from another class. For example a wizard trained in Religion could at level 1 select the Leader feat to replace his Implement Mastery with Healing Word.
That's pretty much it. It's not completely freeform, but it does allow much more freedom than core multiclassing. I'll finish with an example custom class.
BARD
Role: leader
Armor: cloth, leather, hide
Weapons: simple melee, simple ranged
Proficiencies traded for bonus feats: 3
Bonus feats: Defender, Striker, Skill Training (Acrobatic or Thievery)
Defense bonus: +1 reflex, +1 will
Skills: Bluff, Diplomacy, History or Streetwise, Religion (need it for powers)
Class features: Inspiring Word, Inspiring Presence, Artful Dodger
At-will powers: Bolstering Strike (because it uses Charisma), Commander's Strike
Encounter power: Guarding Attack
Daily power: Bastion of Defense
It's not a perfect bard, but for me it will do until we get the PHB2. You can also rename all the powers to feel more bardic (like Inspiring Word would become Inspiring Song and Bastion of Defense could become Ballad of the Last Stand).
If you want more realistic bard you can swap Bolstering Strike with Sly Flourish in which case you no longer need the Defender feat and could replace it with either another Skill Training or perhaps Linguist. You also won't need to be trained in Religion anymore (unless you want some cleric powers) so you can replace it with another skill.