Technically speaking a dual 2 1/4" system has more flow area (7.95" for the dual 2.25" pipes -vs- 7.07" for the single 3.00" pipe). But I'm no airflow engineer so there may be other factors involved so I can't tell ya that it'd be better than a single 3". A lot of people seem to like the 3" single shot systems. There aren't many people that run less than a 2.5" dual system as far as I know, but I do remember hearing quite some time ago of one member that was running a 2.25" dual setup on an 11 sec TB.
I just replaced my older-than-dirt ATR 2.25" stainless cat-back with a 2.50" Torque Tech dual setup. It was getting pretty nasty looking, it was at least 12 years old and the welds in the y-pipe were rusting so I decided to step up.
Steve