I was thinking that an interesting approach to prestige classes would be to eliminate them as they currently exist and instead make them branching options on existing core classes. Say once every three levels gained in a core class the player is presented with the option of continuing on in the core class or taking a prestige branch. A character may never go back once he's started down a branch.
Each branch could offer additional branches as it grows. This would make the core class descriptions much longer.
		
		
	 
The thing is, this isn't really that dramatically different from how PrC's usually operate anyway. Someone takes Fighter to level 5, jumps into a PrC, and then is a Fighter/PrC for the rest of his career, maybe jumping to a similar class if the powers overlap. The different "branches" are different requirements -- a fighter that did XYZ could take PrC (or branch) 1, a fighter that did ABC could take Branch 2, etc. If the PrC is tough to get into (requiring, like, level 10), a character would maybe never go back to his original class.
The vast majority of PrC's out there represent variants on a core class that are specifically suited to particular foci of that core class.
	
	
		
		
			Wasn't Creamsteak working on something like this for his Final Fantasy d20 thing?
		
		
	 
I've hashed out something for my FFd20 project that works in a similar way to FFV, Tactics, X-2, and other "classed" FF games. The thing with this system is that the powers you gain stay with your character, but you can only access a limited number of them at a time when you change classes. The class can drastically change how one character accomplishes things, and cannot be tied well to character level (which advances independantly from class level).
The thing is that it requires 2 simultaneous systems of XP: one for character level, one for class level. The "normal" XP system only raises you HD according to your monster type (usually humanoid). You get more HP, better saves, more attack bonus, etc. The additional XP system (the "JP": Job Points) raises you according to your currently selected class. 
Your currently selected class works something like a template. You gain some of the 1st level abilities of the class, and you gain more class-based abilities by gaining JP. It usually applies a "cap" to your statistics -- e.g.: the Wizard class may halve your hp, cap your Fort and Ref saves at 1/4th your HD, and give you a bonus to Will saves. The selected class would also give you a bonus/penalty to ability scores (in the Wizard's case, maybe a +2 Int, -2 Str).
As a character, you have a certain number of "job slots" based on your HD (two plus one per 5 levels). Your current job fills one of these automatically, and you can fill the other ones with selected abilities from your other jobs that you've gained with JP. You can change your job and job slots after 24 hours of rest.
There are a lot of problems and difficulties doing this on a pen-and-paper system that a computer takes care of really easily -- adjustments in HP, magic power, the categories for your class-based abilities, etc. There's also the verisimilitude question, since most of the characters in those FF games got powers not from their own skill, but from magical artifacts that contained the class powers (making someone who is a rogue one morning and a wizard the next more easily believable). You can literally wake up the next morning and be a nearly completely different character, ability-wise, which is harder to do in pen-and-paper games than on a computer.
So, let's give an example: Thurgood the Dwarf is a 1st level character, and his current job is Fighter. Fighters give you +25% maximum hp, +level attack bonus (maximum of your HD), grants you a bonus to Fort saves but caps your Will and Ref saves, and gives you +2 Strength, -2 Intelligence, -2 Charisma. Every time he overcomes a challence, he recieved XP and JP (usually a lot of the former and a little of the latter). If he gains levels from XP, he increases his HD, attack bonus, ability scores, feats, and saves according to his humanoid type -- 1d8 hp/level, +3/4 attack bonus, etc. This has no effect on what he can do as a fighter. He doesn't gain hp, saves, or anything else as a fighter. He gains them as Thurgood. Let's say he gains 4 Thurgood levels before he's got two Fighter levels. He's a 4 HD character with the powers of a level 1 fighter, but with slightly better saves and hp. 
As a first level fighter, he has access to the class-granted Fighter abilities, which happen to be "Fighter Bonus Feats." Accessing these bonus feats requires spending a job slot; Thurgood has one open job slot now.
When he gains enough JP to increase his fighter level, he gets another Bonus Feat, bringing his total to 2. Let's say he chose Cleave and Dodge ('cuz why not? 

)
Now, he changes his job. He becomes a Wizard. the fighter template is removed (reducing his hp, adjusting his saves and ability scores, removing the attack bonus), and the Wizard template is applied. The wizard template further reduces his hp, re-adjusts his ability scores and saves, and lowers his attack bonus. Furthermore, the Wizard's automatic class-granted Wizard ability is "Wizard Spells," which takes up one of his job slots. He has one open job slot, and he spends it on "Fighter Bonus Feats," enabling him to access Cleave and Dodge again. He gains 3 levels of Wizard (with JP, not XP) and gets acess to "Wizard Spells Lv. 2" which allows him to cast spells like a 3rd level wizard. He does this, let's say, before he gains another HD. So now he's a 4 HD character with the powers of a second level fighter, and a 3rd level Wizard.
Now he changes his job to Rogue. He gains the Rogue job-template instead of the Wizard job-template, and the Rogue has "Sneak Attack" which takes up one of his job slots. He spends the other one on "Wizard Spells," basically making his fighter levels pointless for now. At least until he gainst another HD and gains a new ability slot....
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That said, I do kind of like the choice to "infuse" with certain abilities at certain levels, like the light/dark dichotomy mentioned above....might hafta think about this one....
