That's if you can get past the mediocre 3D graphics on the 3DS version. I mean, I'm a fan of those early 3D games, and even I think it could've been better. There's really no reason why a game that practically LOOKS like a first-gen N64 should be $40.. except precedent, I suppose. The 3DS is full of expensive N64 games last I checked. >_>;
If the price was more reasonable (say, $20 without having to pay extra for all the damn DLC), and I actually had a 3DS, I'd say go for that version. As it stands, I think I'll be getting the Plus version.
I guess if you just can't stand having money, get every version and see for yourself which is best. For me, I'm a gamer with low monetary surplus, so I have to pick and choose my titles wisely. I'm still considering just getting the free original version again, haven't played the thing since it was untranslated.