1) I would say the fundamental problem is that combining modular abilities with tight silos seems perfect from a game design perspective ("Look, I'm creating strong class flavor while still leaving lots of room for customization!"), but most players just don't like it. People who want freedom of options feel overly constrained, people who want fidelity to classic tropes feel overwhelmed by options, and people who value simulation don't like the seeing the interior workings of the sausage factory that much, metaphorically.
2) I understand the premise of the +level to rolls, I just feel like having your level bonus swamp your other bonuses makes your own choices feel less meaningful. Yes, I know that it really acts as a restriction band for on-level challenges and is pretty much illusory, but it just doesn't feel needed. I'd rather see high level narratives supported by feat choices and proficiencies.
3) It feels sad that the really interesting concepts they've introduced, like the 3 action combat and the +10/-10 crit system, are being overshadowed by market-deaf choices in class design. The most popular thing Pathfinder introduced mechanically was archetypes, building a relatively simple base class chassis and then introducing a ton of archetypes to modify them would have been much more well received, I feel.
4) Less boxes. People don't like boxes. Don't put rules in boxes. Organize by good font choices and spacing.