First things first, remember that "criticism" of a port/version of a game is not the same thing as hating on it. Neither is it stating certain facts or making more-or-less realistic speculations about the game.
So with that out of the way, here are my thoughts on the matter:
- The factors of content -
The Wii U is more powerful than the 3DS and it's discs are capable of holding more data because of that.
The stages in the 3DS version have been confirmed only to have 2 music tracks each while the Wii U version has a similar library to the one in Brawl.
The only content which both versions will share are a few stages, the entire character roster, and arguably a few gamemodes such as classic, multi-man, and events.
There has been more of a focus on the content of the 3DS version since that's coming out first. When it's close to be coming out, we can be safe to assume that we'll get a lot of news in regards to the content we'll see on the Wii U version.
So while we know there is Smash run as an exclusive mode and that there are stages which won't be present in the Wii U version, it is quite safe to assume that we haven't seen half of what game modes the Wii U version will have to offer. The larger soundtrack is a nice indication that allows us to be able to deduct that the Wii U will be more rich in terms of quantitative content.
-Technical factors-
The 3DS' multiplayer is based on wireless communication, which the Wii U isn't necessarily. That means that connection issues only are possible for the 3DS version, and it was evident that they are possible when we saw the initial stream during comic-con. There has also been reports of lower framerates when things got hectic, which was not what we were promised. All of that is dependent on the demo build though, so nobody can say for sure that it's a surefire deduction of the 3DS version's technical limitations.
The 3DS version will not give the player the option to use a varied amount of controllers to play the game, which is a set-back from what Brawl offered. At most, we will be able to attach a dual analogue to the game, but that hardly gives the player more choices than switching between controllers entirely. The Wii U will allow the player to choose between the GC-controller, the gamepad, the classic controller, and probably the wii-mote(+nunchuck combo).
Wired online is impossible for the 3DS, most likely making it's online stability less sufficient than the Wii U's.
So because of the way the 3DS is set up, it may well be that it's technical features aren't as flexible as one may think. The rest is dependent on how finished the demo-build was, but that's basic speculation in the long run.
-Personal opinion-
I can't wait for both versions. Love how both look, and how they are playing out so far. Even if I did list those factors above, it doesn't mean I'm inclined to call the 3DS version to be a bad version of the two. I just think the Wii U version is the definite one to go for.
I'm getting both versions, and I'll be playing both regularly. I'm a varied gamer, so I appreciate being able to play smash both on the go and comfortably at home.
