One thing I would like to point out about Cave Story 3D over Cave Story in the eShop is the platforming is a bit rough in some areas as it's hard to tell what's part of the foreground and what's part of the background. Seems like they should have made use of brighter colors that contrast with the background objects. That said, the 3D version does treat you to a great remastered soundtrack from Danny B.Cave Story 3D - Vastly underrated IMO, the graphics style adds a lot of atmosphere to the game and there is a lot of detail to the backgrounds and environments that just isn't possible with the 2D graphics style of the original, other than that it's still the same great game. I don't see where you're coming from with the controls as I've played both and I never felt like the controls were impairing me in any way. The game is hard, but the controls aren't to blame for it.
Just wanted to point out some of the flaws, though it's still a good remake. Also, it's a lot harder to find now and expensive. Generally, if you want to check out Cave Story, I recommend the one off the eShop for 3DS or Cave Story+ from Humble as they're only $10 and are tightly designed. Only go for the 3DS 3D remake if you find it cheap or if you're really into Cave Story.