I think 3D fighters are tons better. They have more depth. I suck at 2D fighters any way.
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They may have more depth, but the feel of 2d fighters i beleive are way more solid. Also 2d fighters, if your not a button masher, are very skill and combo based. 3d fighters are but most people out there just close there eyes and mash.
The only 3D fighter I can get into is Soul Calibur... so I guess I prefer to the 2D fighter. I love old school Mortal Kombat and Street Fighter. And Super Smash Brothers Melee. >_>