Honestly, Cave Story DSi is my preferred way to play Cave Story on my 3DS. I don't need to say much about Cave Story 3D to explain why it's not my favorite of the handheld versions; there are a plethora of issues the game has, and even putting the price aside, it's definitely among my least favorite iterations of the game. Cave Story 3DS eShop sounds like it should be the definitive version, and it is pretty good, but I take issue with the camera. Cave Story DSi does this really nice thing to account for the smaller screen, in that it zooms you in a bit more so everything is more easily visible. I've never had an issue with the screen crunch, so I'll take that over the 3DS eShop's microscopic sprite sizes. Plus, a really underrated feature in the DSi version is the Sanctuary speedrun mode. Unlike the versions seen in other games, this mode allows you to restart from the beginning of the level instead of making you pick out your equipment every time you lose, which is a HUGE upside in my eyes.
Cave Story DSi may seem like a pointless game with all of the other versions of the game that exist, but I think the subtle differences between the other portable versions (Switch version notwithstanding) puts it at the top of my list of portable Cave Story ports I'd prefer to pick up again. I'm quite glad that I bought it when I did.