I'm one of the people that actually liked Cave Story 3D. My heart is always in the WiiWare version though cause it was the first one I played. I also liked the Wiimote as a controller.
WiiWare have some bugs, like Music not loops correctly, or in "Newer music version" doesn't works drums (they updated later in PAL Version)
3DS Version is very detailed, but with some bad models, like Igor, looks a little strange, so my favorite version is Cave Story (eShop version, not 3D)
Oh, yeah, i forget it, Cave Story + is very good, tho, Nemesis Challenge is a hell, i died like +300 deads, and i never can complete that ;O; Some tracks are good, like Meltdown 2, it's a semi-remake from MeltDown (Beta) Or Jenka 2 sounds cool too!, one track i didn't liked is Balrog's theme. but all tracks sounds very cool, incluiding Beta Music, Newer version, and Remasterised tracks too.
Also, other hell is completing Cave Story in HARD MODE with Polar Star. and later convert it to Spur, also only 3 HP xVx i wasted 6 months completing that... and a lot of deads (more than Nemesis Changelle, still i can't complete that xD)
Yeah. Really I think Cave Story + is the most complete version, since it has every version of the music whereas the 3DS only has the original. Plus, Cave Story + has the remastered graphics.
Haha I hope you like it! It's a roguelike game which are usually pretty hard but since you could beat all that stuff on cave story you should be good lol