The biggest point of criticism that the MD version earned was for it's massive slowdowns. This is fixed in the 3DS version, though it would have been nice to have a
sprite limitation option on board to simulate that effect, if only for the nostalgia. Furthermore, you have the opportunity to record your superplay. Of course, now you have a wider screen, too. All in all, nothing you could call significant. As for the rest...
The Graphics are are nicely upgraded, with only the backgrounds looking a bit washed out and poor in contrast in comparison to the Genny and you still have that choppy-like scrolling of the original. Tho the music doesn't sound as good, as through the original Yamaha YM2612, it certainly remains its strength due to accurate adopted compositions. The cutscenes were changed a bit, but not necessarily for the worse and the silent movie feel stays intact. Top scores here overall.
Considering all the occasions, on which they could have ruin this port (just look at
this thrash for comparison's sake), it became excellent, even a small masterpiece.
Here's some good footage:
Edit: I forgot to mention, that the difficulty level has been toned down significantly. The default settings of the Mega Drive original are now found on the "Hard" difficulty on the 3DS version. Other than that, thanks God it isn't different than the Genesis game
.