It is still a class-based system, and I for one think that it's far easier to remove flexibility from design than to add it later. Witness 1e's Unearthed Arcana, 2e's kits (or Skills and Powers), and 3e's prestige classes. All of those options proved pretty difficult to adjudicate (and at least 3e anticipates new PrCs, feats, and such in its design guidelines, unlike the previous two). Having all that stuff built into the game from the beginning allows DMs to pare down by turning options into automatic class features.
For instance, the talent trees. A DM (GM) who doesn't want the complexity of talent trees can just pick a set of talents and make them abilities for the class to take at x level, just as with pretty much every preceding edition of D&D. It'd be like simplifying skills by removing the element of allocating skill points and just awarding all PCs (level +3) ranks in all class skills. Not so difficult.