The controls are different? That sounds unlikely or downright stupid. Vita has everything 3DS has except the second screen so the controls should pretty much be identical. Besides, I heard the 3DS one was glitchy. And you're doing it right, nobody cares about 3D
I think the control problems are related to the touch functionality. Apparently the stylus makes the touch controls more accurate and responsive compared to the finger controls on the Vita. I don't really think that's a huge deal in a VN though personally.
Oh and the glitch is a save bug if you try to save in escape rooms. I think it exists in the Vita version too, but it's either less prominent there or the 3 save slots make it easier to ensure your data against it. Either way, I won't be saving in escape rooms.