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I'm not sure if taking Cave Story FULLY into the third dimension is a good idea. Just doesn't seem to work with the general formula/flow of the game. You'd have to change it up quite a bit for the experience to even be remotely fun. All things considered, try your best! It'll be interesting to see what comes out.
An issue i can really think of, is the enemies in the game. Aside from every critter in the game and the frogs from Grasstown, a whole lot of them will have X7 Syndrome and will provide no threat whatso ever.
CS3D wasn't all that bad imo, pretty buggy and definitely needed more time for animations and bugs to be patched, but otherwise it seemed like a pretty faithful remake of the original. I played through it a few times when I was younger and had a blast.
It is definitely better than CS+ and 3ds eShop, imo. But I'm so biased towards bonus features in the games, I'd rather play Cave Story for Cave Story. (And as a bonus, at least it's more honest with the extra 3 save files with Classic Mode than the four versions with Curly Story included)