I'm trying to decide which version to get and am leaning towards the vita version because... I'm not really sure why. I haven't seen anything of VLR yet. Is it presented in the same way as 999 with mostly static images and text? Is the 3D just the images stick out a bit? The dual screen setup didn't really seem necessary while playing 999 and the Vita does have a bigger screen.

Is there any reason at all to buy one version or the other or should I just wait until one of them goes on sale and get that one?

The Vita Version probably looks better. I never seen either, so can't comment.

There's a memo system that lets you write down notes, which can be helpful when solving puzzles and stuff, so the stylus might be an advantage there. I played on the Vita though, and was totally satisfied. They're probably identical (well, apparently the 3DS version has some game-breaking save bug or something).

The 3DS has better touch controls, but the Vita version looks better (although I would argue that the graphics in this game aren't really that important).

also the 3DS has a game breaking bug that can corrupt your save data. As far as I know it's not present on the Vita.

I can vouch for the Vita version being fine, probably prettier, haven't seen much of the 3DS version. Edit: Apparently the audio is compressed on the 3DS too, so if you're some sort of audiofile Vita wins in that court.
 
3DS version is probably easier to navigate on due to the stylus, also for taking notes 3DS probably wins out (I just used a pen and paper...). Trade off is the save bug that everyone has mentioned.

I played through the 3DS version, as many have said, i would say it would be easier to navigate due to the stylus. That alone tbh is more than enough reason. Also when you make your own notes, you can utlize the two screens by looking at the puzzle with your notes up at the same time, which im pretty sure you cant do in the Vita version.

I've only played the Vita, and I had no issues navigating it. The larger screen makes a stylus unnecessary. It also has trophies, which are actually useful since they track your progress and you don't get the platinum until you've seen all that the game has to offer. And, for what its worth, there were some comparisons saying that the Vita version has superior audio quality.

@Sayishere said:

I played through the 3DS version, as many have said, i would say it would be easier to navigate due to the stylus. That alone tbh is more than enough reason. Also when you make your own notes, you can utlize the two screens by looking at the puzzle with your notes up at the same time, which im pretty sure you cant do in the Vita version.

The notes appear translucently above the puzzle, so you can see both at the same time, that's not really an issue. I also found myself using the L&R buttons to navigate quickly around the rooms (also, the vita screen is pretty big, you can swipe pretty quickly to move around the room), which is perfectly fine.

@TooWalrus said:

@Sayishere said:

I played through the 3DS version, as many have said, i would say it would be easier to navigate due to the stylus. That alone tbh is more than enough reason. Also when you make your own notes, you can utlize the two screens by looking at the puzzle with your notes up at the same time, which im pretty sure you cant do in the Vita version.

The notes appear translucently above the puzzle, so you can see both at the same time, that's not really an issue. I also found myself using the L&R buttons to navigate quickly around the rooms (also, the vita screen is pretty big, you can swipe pretty quickly to move around the room), which is perfectly fine.

Ah ok, well thats good to know. The only other thing i can think of that might be an advantage is writing notes would be easier with a stylus, but thats about it. Seems like both versions are sufficient enough. The Vita version may be the way to go, especially with that sexy screen.

@FancySoapsMan said:

also the 3DS has a game breaking bug that can corrupt your save data. As far as I know it's not present on the Vita.

The Vita version has the same bug, though it seems to be much less common than on 3DS. I don't know if it triggers the same way (saving in a certain puzzle room (PEC) or doing the colored dices puzzle), but I've seen some people online complaining about getting their saves corrupted after the game had crashed on them. Sometimes it's mid-text in a story part, sometimes is inside a puzzle room.

I've played and beaten 100% of the 3DS version without any issues, so I guess it's pretty random. I did close the lid whenever I noticed the framerate drop while doing the colored dices puzzle, though. The best way to avoid the save-erasing bug is to never save inside a puzzle room. And if you're on Vita, take advantage of the multiple saving slots and the fact that you can back up your saves to a PC.

Also, in case you're wondering, I'm using the spoiler tags to hide the name (or, rather, vague description) of the puzzles and rooms involved in this bug. It's completely safe to read them, but I guess it's just common courtesy to avoid giving any kind of unsolicited information :P