MGS3DS made a lot of sense at one time. Then the project moved from KojiPro to an external porting team, got severely downgraded (even though the original demo was running on weaker hardware than what the 3DS actually came out with), and Kojima became enamored with the Vita and focused on putting the HD Collection there instead of the remake MGS3DS was supposed to be.
It basically went from "This will be awesome" to "I guess we have to make this?" in months.
I own it. It's probably the worst version of MGS3 out there by a mile. There was weirdly a 3DS firmware update that helped the framerate a lot, but that was only one of the game's problems.