Just finished the JP 3DS demo, here are my comparison impressions for anyone who wanted more information before deciding which version to get. 3DS version was played on an LL:
Graphics:
Vita is super crispy, great colors, dat OLED etc., but at the same time some of the upscaled assets, especially certain environmental textures, look really blurry and out of place in contrast to the rest of the graphics (Alice's boobs look like they're melded together at the seam rather than 2 separate melons).
3DS version's 3D is excellent. I usually turn 3D off in games but it looks GOOD here and I ended up using it the whole time. The resolution/blurriness is nowhere near as bad as
this blog post made it out to be. The textures and everything also look natural at the 3DS' resolution.
Controls:
Both versions have the same options for the mechanical controls - L/R to turn camera, analog stick/slide pad to move the target cursor, face buttons to select objects/advance dialogue, dpad for menu shortcuts etc. (Vita analog is more sensitive than the 3DS but both are still over-sensitive imo).
The Vita's finger touch controls are a little less responsive than the 3DS' stylus and straight up terrible for writing in the scratch pad in comparison.
For the 3DS my number one gripe is that the touch controls are on the bottom screen, but the main room view is on the top screen (as opposed to 999 where you looked/interacted exclusively with the bottom screen during escape segments). Both screens actually show the same view, but the bottom one is covered in an intentional blue scan lines effect and much smaller. What this means is that while the clear, big, 3D image is on the top screen, you're only going to be looking at the more obscured, smaller bottom screen when clicking on objects and interacting with the environment.
The bottom screen's scan lines effect in combination with the reduced size can obscure small objects pretty easily depending on the background color. At one point I could see a small key on a blue table on the top screen, but it was nearly invisible on the bottom screen. This creates a disconnect since you either have to be constantly looking back and forth between the two screens while navigating/interacting if you want to enjoy the visuals, or just deal with looking at the scan line filtered bottom screen the whole time.
Here is an example of what I'm talking about:
http://www.cubed3.com/media/2012/October/VLR_Screen_1.jpg
Sound:
The 3DS version definitely has compressed audio and it's very noticeable to the point where I was surprised how tinny it sounded (I used headphones for both versions). It's mostly only a problem with voiced lines but the difference is there. Not sure if this will change in the US release or with the dubs.
Overall it feels like a tossup right now, but I have a feeling buying a capacitive stylus for the vita version might be the best way to play, not just because of the crisp visuals and higher fidelity audio, but for the ability to interact with a big clear screen all the time rather than an obscured one. Without a capacitive stylus though the 3DS version would still be worth putting up with imo since finger controls just aren't that good.