The new visuals will leave players split. I personally like the new, spiffed up 3D characters and environments. The switch over to polygons could have been a disaster; the collision detection could have been thrown off, ruining one of the game's major mechanics. Thankfully, this doesn't happen.
Additionally, the original look had a certain charm that is hard to translate into anything but polygons. How successful Cave Story 3D is at keeping the original's charm is largely up to the player. Again, I like the look, but have read just as many negative comments. I like the added depth and detail.
As for the 3D effect, it mostly adds depth to backgrounds. It's a really cool effect and gives the sense of scale. Even with the effect, I ended up playing with 3D turned off maybe 50% of the time.
The soundtrack will also leave the fanbase locked in civil war. The original soundtrack, like the visuals, had a certain charm that endeared itself to fans of the original. Along with the polygons, Cave Story 3D adds a remixed soundtrack. It's the same tunes, but with a "synth-ier" vibe. I was cool with the visual upgrade, but I'm not completely on board with the audio. Call it nostalgia or taste, but it's the same reaction I have whenever I hear a redone version of the Super Mario Bros. soundtrack. I'm used to hearing songs a certain way...