All skills should be class skills. Each class is meant to be a flexible rules set, so a person who is a Fighter by the rules might from a roleplaying perspective be a carpenter who just happens to have a knack at brawling. The Expert gets enough skill points to be good at a lot of things.
Everyone gets any four feats at 1st level. Fighters use this for armor, magi for metamagic and item creation, experts for whatever they want. This includes weapon and armor proficiencies. It's all very flexible, so if you want a 1st level magus with sneak attack, you can do it.
Fighter: Good BAB, one good saving throw, d10 hp/level, 2 skill points/level, 1 combat feat at 1st level, and every even level.
Expert: Poor BAB, two good saving throws, d4 hp/level, 12 skill points/level, bonus feat every 5th level.
Magus: Use the current sorcerer mechanic for casting on the fly, but use the Wizard spells per day and the wizardly mechanic for learning spells. Every spell is on the same single spell list, though we might need to change the level of a few. You can learn as many spells as you want, and don't have to pay ungodly amounts of money to learn them. A priest of a temple of healing could just read the holy scrolls of magic and learn how to cast cure light wounds, or a demon-summoner could be taught a spell by a demon he conjures. Poor BAB, one good saving throw, d4 hp/level, 2 skill points/level, 1 magic feat every 5th level.
It's up to the players to describe what their class levels mean. An Expert could be a scholar, or a skilled tracker, or a guy who grew up on tough streets and learned how to survive. You'd have things like sneak attack and possibly rage be feats that fighters could take, and for spellcasters, you could either play a generic mage with a little combat, a little summoning, a little healing; or you could play a traditional druid or cleric by picking a limited list of spells.
For example, a barbarian would be a standard fighter, picking the right feats.
1st level--rage, light armor, medium armor, shields, fast movement.
2nd level--Toughness
4th level--Rage
6th level--Toughness
8th level--Rage
10th level--Toughness
etc.
A rogue would be multiclassed.
*Expert 1--lots of skills, pick the Sneak Attack feat, light armor, a few weapons, and maybe the toughness feat.
*Exp1/Ftr 1--evasion feat
You then continue at a ratio of 1 Expert levels per 1 Fighter level.
A bard would be:
*Expert 1--perform skills galore, expert knowledge feat (lets you use your class level for untrained knowledge skill checks).
*Exp1/Mag1--pick up some spells to emulate bardic music
*Exp1/Mag1/Ftr1--get some fighter feats.
Repeat with the same ratio. I think it works very well.
