LokiDR: Well, I admit that you have caught me on one thing - I don't like the PrC and classes like OoBI, Master of Chains, and Weapon Master are poster children for why I don't like it. Actually, I find those classes even worse than the duelist, because you can't argue that archers or spiked chain wielders need a class focused on them to make the concept viable.
I do generally feel that PrC's are 3rd ed.'s one big design mistake. Third ed. went a huge step away from having each class be a single stereotype individual basically identical to every other person with the same class, and towards flexible customizable character creation and development. Third ed. took a huge step towards making all classes equally fun to play and equally useful and balanced against each other. Yet in the middle of this, it decided to drop in these rather unflexible, personality confining, unbalanced classes. Not only does this undo much of the work that they accomplished, it flies smack in the face of the notion of the CR/EL/ECL system they tried to develope to help DM's. If PrC's are really supposed to be more powerful than core classes, then this means not all 4 member Xth level parties are equal in terms of CR or EL. This shoots a huge hole into an already holey system.
If you really wanted 'advanced classes' then you should have only given the core classes 10 levels of progression as was done in D20 modern. Even that isn't fully satisfying to me, but it would be better than what they have now. What we have now are the core classes, and then PrC's - which are core classes that gain more feats than regular core classes. Ei, there are 'fighter' PrC's that are just fighters with more bonus feats than one every other level, and 'spell caster' PrC's that are Wizards with more bonus feats than one every 5th level. There are some others types, but I think in practice no one ever plays those and they are relegated to NPC's if they are used at all.
I do think that the vast majority of PrC class abilities can be converted to feats. Those that can't are either too good to grant to anyone (the various bonuses damage granted to a Master of Chains for instance, as if the Spiked Chain was somehow a weak weapon as defined in D20), or else can be fiddled with by limiting them or breaking them into two or more feats (X, Improved X, and Superior X).
As to a Wizard taking say Enhanced Mobility, what is wrong with that if the Wizard has a +8 BAB, 5 ranks of tumble, dodge, and mobility? Maybe few wizards will have such things, but if they qualify why not? After all, a wizard _could_ (if they wanted to) have Great Cleave. Nothing prevents it. It just isn't the usual path of development. But if I want to do it, I can. For that matter, a 12th level wizard could probably take levels of Duelist. What I am saying is that if the color and crunch of Duelist were made into feats, he could do so and we wouldn't have to worry about making 'Duelist' classes with full spell progression and them being too powerful. The limited availablity feats would naturally balance such things. And we certainly wouldn't have to worry about core classes becoming obselete after a certain point.
But I agree with kigmatzomat that your arguement against what I have to say, other than the fact that I am indeed argueing against the concept of PrC's in general, is somewhat erratic.