I think this topic needs to be brought back to attention.
I heard from the person running the Soul Calibur tournament that he was going to ditch SC3 in favor of SC2 this year. Now, if it was a landslide vote in favor of SC2, I'd kinda understand, but check the votes above. I think we can assume that the 3 people who chose the third option are in favor of SC3. Thus, the majority of the votes are for SC3.
I'm perfectly fine with having an SC2 tournament. After all, I won the last SC2 tournament, so I must be doing something right.
In fact, I play much better with my three favorite characters from SC2 than I do with the same three characters in SC3. However, I have not touched SC2 for months upon months because I never expected SC2 to ever come back and replace SC3 at the con. Many others will be like me: we enjoyed SC2 plenty, but we're hella rusty because we've moved on to SC3.
As for game quality, I can see arguments on both sides. I don't think SC3 is more unbalanced, but it does have greatly simplified move lists with fewer branching combos, and fewer combos overall, many of which I actually used in SC2.
My vote is for two separate tournaments. Both games have had sufficient popularity to justify their own tournament, and I think SC3 is nowhere near bad enough to rationalize its cancellation.