They feel and shoot very differently.
I have an M9A3, and it even feels a bit different than a normal 92/M9. It doesn't take too much to alter how a pistol feels to shoot.
I like both pistols... But I think the 226 is a smoother shooting pistol. Though the M9A3 has some improvements in the trigger, not in the older pistols, and that trigger is better overall.
I recommend a 226 with the SRT trigger in it. I much prefer it over the standard trigger.
I know there was an updated part for the SRT trigger, that prevented an issue where the trigger would stop resetting properly. This was caused by damage to the part in question, over time. The new updated part was shaped differently, and prevents the issue completely.
I had to install the new part in my pistol, but new production pistols may already have the part, as it was a couple years ago now, when it was released.
I don't know 100% though, so I asked over at the sig forum. I will report back later.
Here is a post that describes the parts in question.