2D. The little of 3D ones i've played is an absolute clusterfuck of particle effects and the camera and spacing of 3D fighting makes it harder to tell if you're hitting or not.
I have played several 2D fighters, UMVC3, BlazBlue, Persona 4 Arena and Skullgirls in the 3D corner is... Soul Caliber 4. Yeah, not the best balance. I will say ring outs are fucking hilarious though. Especially any dive moves that can unintentionally ring out yourself with.
I still love the troll move of winning a round then during the last few seconds of movement, dive headfirst off the stage for no reason.
ArcSys has the 2D mechanics down well, I think Persona 4 Arena has the best balance of mechanics to date. Autocombos cost health and overall do relatively little damage, everyone has a move that relieves pressure but it costs health and spamming it is the fastest way to die (looking at you Shadow Labrys,) the passive Awakening comeback system is as fair as it is genius (I think they're continuing it in Chrono Phantasma with Overdrive) and every character is viable. Except Elisabeth. Elisabeth has some fucking MAJOR flaws.
Also BURSTS! EVERY 2D fighting game needs a Burst mechanic, it makes things way more fun. Seriously, if Skullgirls had a proper Burst instead of this shitty Infinite Protection System it would be really fun. Nobody likes being on the receiving end of 20 second combos, everyone has them and the community has found a way around the IPS so it never procs which ironically only makes touch of death combos worse.
Oh and when the IPS does activate, it's unsafe as fuck and if the guy has a combo that damaging he'll account for it and just block it. So it's not only worthless it's a free reset.