Yeah, that was kind of a pain to deal with...
My only other (minor) grievance with the game is the way they changed the capsule placement. Like, I'm not entirely against the idea -- doing it for Hard Mode, for example, might have been neat -- but the original game was just borderline perfection to me, so much that any kind of change like that is like smearing your fingers on a work of art.
Definitely recommend 3, it's my favorite of the series. Only one I played to mastery, too.
On-topic, but unrelated:
I want that Staple shirt so much (all of these, really, but especially that), but I can't afford it right now, and it's a limited item.
I could totally see Nytetrayn wearing that, too, and besides his hat, he's never even worn clothes that aren't black. XP
Sigh.