I really liked the 3DS Version, the D-Pad have a good precision on timing, the stick is more confortable to me. Also the Game includes lots of costumes that you have to pay for them on the other versions. The 3D mode its Good, but I rather preffer turn it of on the Options because it blocks the game to 30 FPS, turning off the 3D will make the game playable in 60 FPS. Its Glorious.
The downsides... I dont like the super moves on the touch screen, there are many many MANY noobs Online spamming Sonic Booms+Flash Kick with Guile, Hondas slams and headbutts, Adons and their Jaguar kicks, ITS ANNOYING, but the most frustrating is the AUTO-BLOCK, you can punish players because the block automaticaly and can recover from the block stun spamming attacks.
Fortunately, you can play online with people with the SAME configuration of your buttons PRO or LITE, I recommend you to use the PRO.