Rather than level completion themes, you know what I'd love to see more of in Smash? Peaceful village themes (and god knows there's a LOT of them among the represented franchises). I guess most of them aren't very fitting for battle outside of remixes, though they wouldn't seem very out of place if we had towns or something in an Adventure Mode. The facilities in World of Light were kinda like that, though I think it'd be awesome if we could get to walk around towns and other non-hostile areas (I imagine something like the towns in Castlevania II and other 2D action-RPG-ish games).
Why are you talking like this is 1993? Seriously, as others have pointed out, NIntendo have personally become co-owners of the Bayonetta sequels and the Fatal Frame series, and even going back to the GameCube days, I think they struck up an exclusivity deal (albeit a temporary one) for Resident Evil 4. Hell, I think they dropped the prudish act as early as having Mortal Kombat II on the SNES (after Mortal Kombat 1 was pretty much mocked and ridiculed as being the tame version on their system), plus it was mainly a Nintendo of America thing to begin with.
Eh, different strokes, I guess. While pre-rendered sprites were more of a compromise due to the fact that the SNES couldn't handle true 3D (at least not without being extremely limited, as the FX games were), I found them nevertheless impressive for what they were, and think they still hold up pretty well today. Though, I would agree with you if you were talking about pre-rendered sprites on the Game Boy, and even the Game Boy Advance (I really don't think GBA did the Donkey Kong Country games justice, at least from all that I've seen of them).
I'd also agree with you comparing Super Mario RPG to Square's other SNES games, though mainly because the Square RPGs of those days were setting the bar pretty damn high on how 2D sprites could look. Final Fantasy IV seems like an exception, however (maybe it's because it was released VERY early in the SNES's life, but I swear, FF4 almost looks like an NES game with a mildly higher color palette.... and in fact, it might've began development as an NES game, if I recall correctly).
After Wonderful 101 and Fatal Frame, I guess Nintendo's loosening up a bit on exclusivity, at least when it comes to their co-owned properties made by third party developers.