Well, Exen, I'm hoping that the talent trees will be easily customizable to make designing a new class into just following a specialized path for a pre-existing class. These talents could perhaps be things that would normally merit a new prestige class because they are clearly more powerful than a feat and don't really fit into the 3E stuff except in a new class. For example, the abilities of the Dragon Disciple in 3E aren't really things that would work as feats, so it became it's own class. However, I think a well-designed talent tree for a class (or for all classes) would be able to allow for the "you grow scales and your AC goes up" and "you gain a breath weapon" without seeming like overpowered feats.
This talent tree idea should apply to creating new base classes too, not just PrCs, so that the base classes can be VERY general but the possible talent trees are only limitied by what you and your DM work out (or what WotC releases as additional material).