RANT ON
Well, I'm going to flat out lay down the flame bait that 90% of all PrC's are broken, and even among the 10% that don't render core classes obselete they are still (by and large) more powerful than core classes. You may feel that that is the whole point.
I feel it was a bad decision in the first place to make PrC's more generally powerful than core classes UNLESS the game was designed right from the start that no one would take a core class beyond the first five levels or so. However, in my mind, a few broadly adaptable balanced and capable classes is a far more elegant solution than a 95 indepedent, specialized, classes which cannot be tested against each other, nor can any new game element be readily tested with or against all classes. Any PrC that could not readily be adapted to a core class lacks sufficient flavor or else too overlaps a core class. Any PrC that covers a broader range of character concepts than a core class, implies either that the PrC is a core class or the core class is poorly designed. Any PrC whose special abilities could all be turned into balanced feats, never should have been made into a class. Any PrC whose purpose seems to be to duplicate a core class but allow by comparison additional feats or feat equivalent abilities over a given number of levels in order to create characters with 'Anime style'/k3wl/comic book/superhuman abilities at a lower level than they would otherwise acquire them is simply tossing the game balance out of the window, not to mention by thier mere existance pushing a campaign towards that anime/comic book/super human/flashy style.
Simply accepting the existance of the concept 'prestige class', pretty much forces your campaign into that style. At best, you end up with a Monte Cook style 'thinking man's hack-n-slash'. At worst, you end up with { phrase deleted because it really is too vile for this board }.
Even the very phrase is to me offensive. Had the original concept been 'advanced classes', it would have been clear that the purpose of the classes was to simulate 'advanced training'. But it is clear that professions and advanced training was NOT principally what they had in mind, but juvenile player ego boosting and ego building power gaming. They had in mind right from the start creating those obnoxious gamers that say, 'See how cool _I_ am, _I_ have a half-dragon fighter/butt-kicker of doom with a +5 keen greatsword of dire slaying. See all the cool powers I have. _I_'ve got a +55 BAB.' And it shows in the design of the classes.
And as I've said, even the notion of 'advanced classes' is an inelegant old school solution that leads to more problems in the long run and just tries to cover up for some basic design flaws in the core classes. It is clear to me at that Ranger went only half-way to a solution, that the game needs some more extensibility in the early design of characters, that more feats were needed in the initial core book for the sake of diversity, and that classes like Druid, Barbarian, and Paladin weren't daring enough in thier revised designs. Too many of the core classes have flavor that is more specific than the flavor of many prestige classes. What 3.5 needs is more feat chains replacing prestige classes, more flexibility in the character design at first level, more guidance in creating variant classes, and Druid redone as Shaman, Barbarian redone as Fanatic, Ranger redone has Hunter, and Paladin redone as Champion. Core classes should be built around profession, not flavor. Prestige classes, if they are allowed to continue, should be variant classes built around more flavor and more campaign specific flavor.
In point of fact, ANY PrC introduced outside of a world book is clearly a bad design, and that includes ALL of the PrC's from splatbooks, class books, player's option books, and virtually any other place that they are customarily introduced. How can they be a tool for a DM to add flavor to the world (the reason presumably they are in the DMG), if they are primarily introduced as a PLAYER option? How can you possibly claim something as devoid of flavor as Duelist or Assassin is a PRESTIGE class? In the case of Duelist, aren't what you are really dealing with is a fighter trained for a certain kind of combat and shouldn't thier be feat chains to provide for that?
So to me, allowing free multiclassing into a prestige class just makes the whole concept that much more absurdist in the first place. Not only do you get more power, but you suffer no penalty for it. Not only do you min/max, but you can freely min/max the exacts levels that give you the most front end abilities for each given class. And lets face it, ALL classes are front ended to some extent just to insure that they have thier basic flavor as soon as you take the class.
Treat prestige classes just like other classes in every way. Better yet, do away with the concept and make increasing levels and increasing prestige one and the same.