Masteries from Everquest OA Frontiers. You choose a percentage of your xp to go towards class advancement and masteries. It's an MMORPG so classes and leveling are exactly what you expect. Masteries were more like feats that gave you bonuses to attributes, resistances, mana/stamina, etc. There were also class and race masteries as well as masteries for things like being a were-animal or were-hunter.
Feats themselves aren't anything new, but the way you could go all in, take a balanced approach, or totally ignore them was awesome. I can picture it being a way to grab feats as well as a method for upgrading things that you first unlock diagetically (I'm 70% sure I'm using that word right) like lycanthropy, titles, mysterious powers, professions, etc.
For base building I like using Numenera Discovery as a resource. I've used it as a base (pun intended) for building in multiple other systems.
VATS even if I have no idea how I would implement such a thing.
Dragon Age Inquisition's guard/barrier mechanic, Mass Effect's armor/barrier, or DOS 2's physical/magic armor. Unlike THP the benefit I like from these is the ability to resist certain effects while my protection is up, different attacks being more or less effective against them, and acting as a in-game reason why that greataxe didn't leave me in multiple pieces.