I've got a couple of conceptualizations that I'd like to see changed, right off the bat:
Divine vs Arcane magic distinction. Get rid of it -- it's arbitrary in the first place and becomes more meaningless and meaningless over time. The only real driving "logic" behind it is that "wizards can't heal." There really isn't much more to it and as more new Cleric domains are created, there are fewer and fewer wizard-only spells left.
All of the "x times per day" stuff. It's completely arbitrary and illogical and creates goofy rationalization about how Elves only need 4 hrs of meditation to rest, but have to spend another hours doing NOTHING before they can prepare spells again. That's goofy. And spell-like or supernatural abilities that can only be used x times per day are even weirder, as it makes one wonder who or what exactly is imposing these limits?
One conceptualization that I would like to see is a reduction in the number of base and prestige classes that you need to create to get a specific character type. The proliferation gets a bit out of control after a while, and we're getting a lot of redundant ones where it makes little sense to have both in the same game (Holy Liberator vs Paladin of Freedom, Spellsword vs Duskblace, Knight vs Cavalier, etc). I loved the idea of prestige classes when I first read about them, but I've been really disappointed in how they've been implemented.
Rather than have a set of core base classes that advance from levels 1 to 20 and then a set of prestige classes that can advance (generally) either 3, 5, or 10 levels. But they currently have to be balanced so that they aren't so good that it's a clear-cut choice to advance in that class instead of your original base class. And for a character like a Sorcerer, there aren't a lot of reasons to go back to advancing as a Sorcerer once you've taken pretty much any prestige class with "+1 spell caster level of existing class."
And really, if you are a Wizard or an Sorcerer and have finally achieved the reknowned Archmage prestisge class, why should you go back to the basics?
Even before 3e came out, I was an advocate of having a small number of base classes -- your typical Fighter, Magic-User, Thief, and (maybe) Cleric, and then creating all specialized character types via skill and feat selection and prestige classes. And that approach could work, I think:
When you create a 1st-level character, you would have a fairly small number of choices of base classes: Fighter/Warrior (obviously trained in combat), Rogue/Thief/Knave/Scout (your nimble, swift and/or sneaky character trained in a multitude of non-magical non-combat skills), and Apprentice (just learning to cast magic spells or spell-like abilities). Perhaps there could also be an Artisan (expert, craftsman, entertainer, etc), a Noble, and a Scholar (well-educated but no magical abilities) class as well.
Unlike the 3.x base classes, these new base classes do not have full 20-level progressions, and instead top out at perhaps 3-5 levels. These classes would have some alternate abilities (such as given in the Player's Handbook II and Unearthed Arcana) to allow for customization, and characters would receive feats a little more often, and perhaps gain more skill points -- at least in these basic classes.
Once you hit the limit in these classes, you would then need to select an advance ("prestige") class to continue advancement. Now this is where the more specialized classes appear. For example, if you wanted a character who was a Ranger, then you would have likely started out as a Warrior or Rogue/Scout. By the time you hit 4th or 5th level, you would have some combination of those two classes to provide the basic Ranger abilities... melee combat, use of the bow, stealth and the ability to perform a "sneak attack," survival skills, riding, the tracking feat, etc. When you take the "Ranger of the North" advanced class, you can advance through to 20th level, gaining abilities that suit your more specialized role but building on what you obtained in your basic classes. Or if you have all of those base abilities but aren't interested in the druidic spell-casting ranger, you could choose a Hunter of the King's Watch advanced class instead and focus on the pure non-magical skills.
All spellcasters would require 2 or 3 levels of the Apprentice class to gain the background in magical study required. Once the prerequisites are met, you could take advanced classes such as Illusionist, Healer, Druid of the Sacred Groves, Embermage, Spellsword (with enough Warrior abilities), Beguiler, Conjurer, Master of Shapes, Warmage, Artificer, Savant, Necromancer, etc).
Your basic Rogue/Knave/Scout class would lead to advanced classes such as Assassin, Bandit, Thief-Acrobat, Bard, Fence, Swashbuckler, Dread Pirate, etc.
Missing from all of this is the Cleric. If there is no divine/arcane distinction, then the Cleric need not exist as a class. All spells would be learned and cast in the same way -- which should be campaign-specific, and unless the DM wants to have a dozen and a half entirely different rationales and methods for spellcasting, she can just pick one that fits the tone of the campaign or culture.
Characters who represent divine agents on earth would be realized as advanced/prestige classes with granted powers (rather than "spells" as we know them). A member of any class could be a priest in a church, but only a very select few have the divine favour to be agents of their god(s), and their powers don't simply replicate existing spells.
And then there could be high-level, "super-prestige" classes such as "Archmage" or "Divine Champion" that are for characters who have mastered (or nearly so) their more advanced professions. Why would an Archmage ever want to go back to just being a "Wizard" or "Sorcerer" once they reach that point? (Because the books only give them 3-5 levels of advancement and they're done, that's why).
Everything builds on the foundation of the base classes. The abilities which you will learn as you advance into more specialized classes are "set up" by how you work your optional class abilities, multiclassing, and feat/skill selection. By the time you take that advanced class at 5th level or so, you have already built the basic archetype of the advanced role you wish to play. And also, there is nowhere left to go in your original class, so the advanced classes are balanced with one another, but don't need to be so concerned with not overshadowing what you get as a 14th-level Sorcerer or Fighter.
The advanced classes can be built so that you don't need the flavourless prestige classes like Mystic Theurge that exist only to accomodate the game mechanics needed to multiclass a specific class combo. With only a handful of level available for these base classes, the loss-of-specialization penalties for multiclassing are pretty minimal and are easily compensated for by choice of advanced class.
If "Spellsword" is your advanced class representing the warrior-mage archetype, then you don't need to worry about Fighter/Wizard multiclassing and how lousy their spells are, feats to help keep the caster level relevant, the Duskblade class to handle this sort of character from first level, but also a Spellsword prestige class to handle this type of character when Duskblade wasn't an option at 1st level.
In the current system, we have a few very culturally-neutral base classes (Fighter, Rogue), generic but still Western-based (Cleric, Wizard, Sorcerer), and then some classes that start to fill very specific roles (Barbarian, Bard, Druid, Ranger, Paladin, Monk). But the prestige versions of the Ranger, Paladin, and Bard in UA are kind of poorly done, and players might find it a long time to be able to take on those roles. The base classes which I proposed are more culturally-neutral and are intended to be flexible enough to build up the major archetypal abilities (or prerequisites anyway) to build on once specialized roles are taken on. It would be easy to tailor any of these to an Asian-themed setting, for example, and including Samurai, Sohei, Shugenja, Ninja, etc as the specialized classes.
Ack, it's getting late. I hope that was coherent. Basically, the bulk of the character's adventuring career will be spent in the advanced/specialized classes, while the basic classes will be left behind quickly (maybe only 3 levels of them). These more mundane basic classes could be integrated with some of the NPC classes as well, to streamline things a bit. There is only a certain degree of expertise than can be gained with that level of training, and anything higher than that roughly 3rd level requires advanced training and/or the extremes of life-or-death adventuring.