I have already played the original PC version, that ported to the PSP, as well as the Wii version, and was interested to see how Nicalis handled the game in stereoscopic 3d. Thankfully, it's very good, with only a few areas that stand out so far you need to turn the 3d slider down. The levels are all redone very well.
The thing I thought some people would like to know however, and the reason I'm writing this post, is that there are 2 extra areas in this version of the game. They are transitional areas, in that they don't have any new guns or story items, but they are fun to play through. There's also a tiny hidden area they threw in as well where you actually can get a new item exclusive to this version. I won't actually detail this for spoilers sake, but if you must know, there's always Google.
That being said, the game is worth getting if you have a 3ds. Who would have known Pixel would reach this kind of success this many years later?