I agree about the 3DS version's 2d gameplay being superior compared to the HD version. The physics are way better and satisfying to such a degree where you wouldn't complain anymore(well except for the purists)
Earlier on I wrote the game off because first impressions made me think it was going to be the lesser good, crap version made by Dimps. But it has great stages, nice controls and great bosses.
I think the only reason now why I prefer the HD version is because of it having more content. The 3DS game is really low on content sadly. However it's got some great visuals imo. The levels have been recreated quite amazing. Stages that arent in the HD version like casino night and emerald coast look really great on the 3DS. And also have some clever level design. I especially like the 3d levels remade into 2d classic lvls. Really cool stuff