I woke up and realized that I forgot a huge one from last night.
Sub-weapons don't do nearly enough damage on bosses (on Hunter), even if you get their weakness. Usually it's 2-3 damage at most uncharged, at which point you're basically just better off using charged buster shots (because you have an infinite amount of them).
I'm watching a friend stream the game now, and he just found out that *charged* sub-weapons do a ton of damage if you get the weakness correct. But that's not how it should work. What if you find the head chip that allows that very late?
Oh, and one last thing. The secret weapon. The input timing is *very* precise, and it shouldn't be. If you go back to the game you got it from and test it out, you'll find the timing is much more forgiving. Because of it being super-precise it's almost un-usable in its current state.