Obviously with no Multiclassing, the concept of a favored class is nonsensical. But in eliminating it, I think Paizo has eliminated one of their more underutilized design spaces.
A while back I created an expanded list of favored class bonuses which included new universal bonuses and class-specific ones that could be taken by anyone with the relevant class features. After implementing the system in several games the response has been overwhelmingly positive.
I think 2E would benefit greatly from having a similar character resource, one with the flexibility to spend on a variety of things, but coming in smaller units than whole feats. For example, you can't simply learn a language as things stand now, you have to spend a feat to learn 2 at once. Languages aren't worth a whole feat, but that's the only unit of character building currency we have to spend. There is clearly a gap in the system that should be filled.
Skill points are gone, but spell points and resonance are now here. Proficiencies could be purchased. Uncommon spells could be learned. Feats could be saved for. There's no real limit to what you can do with it, and it all expands player choice, customization and the sense of progression.
A bonus every level, to be spent or saved. That's all I ask.