It might've been due to the update deleting locally stored trophies. Same thing happens when you switch accounts, but there's no warning here that mentions you'll need to manually sync trophies before updating. Either a firmware error or hilariously stupid oversight.
and going from using my 3DS lately back to the Vita, I think I actually prefer the face buttons on the 3DS. The face buttons are the one part of the Vita's hardware design that's lacking. Buttons are really small, stick out, and sit too closer to the right analog stick. For such a large system it's odd to have these tiny bumps all cramped together.
edit: I think it's just the position. I checked my PSP Go and while those buttons and flatter and clickier, they're roughly the same size and I never had a problem there. the reason it isn't a problem on consoles isn't just the size, but the right stick is far more leftwards. maybe putting the stick over the buttons would've helped if they're on the same level, but there's only so much room to work with.