It feels like the "sweet spot" is so much smaller than any of the other launch games, and even when I feel like i'm in the right spot there's a lot of ghosting and double imaging on the characters.. 
 
Typical lazy launch port, but It seems weird that they could even get this basic thing wrong that most other launch games did well. 
 
As for the game I never played it back then so it's really fun. I actually think it's really cool seeing these old dreamcast/n64 type environments in 3D.

I haven't noticed many problems.  However, one thing that you didn't mention is that in the original game, some objects such as the mosquitos were actually 2D drawings rather than 3D objects.  This is more obvious in the 3DS version, and although it doesn't really break the illusion of 3D, it feels a little inconsistent because these 2D drawings look like cardboard cutouts in the 3D environments.