It won't sell well on 3DS. It's not an interesting fight, honestly.
On one hand you have the Vita ver. which functions like the console versions. The graphics are better. And every Vita owner can play it.
Then you got the 3DS ver. which looks more like a PS1 game. Its more limited than the PE version of Minecraft. Limited size like the PS3/360 ver. -except smaller. Also iirc, it will have limited online play. On top of that, only works on the 'New' line of 3DS.
I like Minecraft and will also be picking up the 3DS ver. too, but I do not believe it will win, sales wise, against the Vita. If it does, it'll win, just barely. Keep in mind the Switch is slowly going to phase out the 3DS, so it hurts sales potential on that front too.








