The long answer is no. There's no 3D* and the game is mostly similar.
... however, there are a few differences in the game proper:
- Grandma Ulrira no longer has her "YAHOO!" shout; it's been replaced with "HELLO!" and "YIPPEE!".
- Effects that make the screen flash (e.g., capacity upgrades) have been slowed down greatly, like most other Virtual Console games.
Wart Mamu's song loses the spotlights, which were done by rapidly dimming the screen (like above)
- You can no longer push A to (try to) print pictures. The game will simply pretend it wasn't pushed instead of displaying the Error 02 message.
- The music is very slightly different in some places due to poor emulation
- The sprite ordering is slightly different sometimes, so things appear in front of things they shouldn't, also due to poor emulation
This list is by no means exhaustive and probably will never be unless we get to see the actual ROM itself, but for the most part any changes are really minor and don't affect play.
* Holding Start or Select when startnig the game will render the game at original size (no filtering) with a faux-Game Boy Color border around it. The game screen is slightly sunk into the border using 3DS's 3D effects.