It all depends on how you want to carry it. I chose the 2 1/4" for my SP simply because, for what I wanted it for, the 3" wouldn't have worked out at all.
I bought mine to carry as backup on duty when I work at the PD and for off duty carry. When carried on duty, it is carried in a holster strapped to my body armor. For this use, 3" was just too long and would have stuck further down than my belt line. 2 1/4 is actually pushing it and, when sitting, the muzzle rides on the top of my duty belt.
If I was carrying it strictly IWB, then the 3" would have worked out just fine. With the 3", you get a longer sight radius and, likely, less muzzle blast and flash, meaning it should be easier to shoot well. However, it may be incompatible with your carry style, so check it out before buying. Either would do you just fine, as long as they fit in with your carry style.