I have to agree with the people who say "it depends".
In my case, the 5" Gov't model is much more comfortable than any .45 ACP revolver I have ever fired. This is not to say that the revolvers are abusive, (though my M1917 Colt with its original grips is a handful), but that the autos are more comfortable to shoot than the revolvers.
Yes, I have chronographed a variety of both, and in my limited experience, the 5" autos produce the same velocity with the same 230 grain ball as the 5 1//2" guns. My 625-8 5" is a tad slower, and a 4" I got to play with was slightly slower still. I tend to think of the 5" and 4" wheelguns as Commanders ballistically. Yes, I know that my sample is limited. Yes, I know some of you have .45 ACP wheelguns that out perform your Gov't models. I still believe the trend is for the 5" Gov't models to produce slightly more velocity.
As far as perceived recoil, the wheelguns outkick the Gov't model, for me. Others tell me that I am crazy. My Colt is almost uncomfortable with the original grips, but much more comfortable with Pachmayr's. The S&W M1917s are also uncomfortable with the original grips, but more manageable with more modern grips.
All of my above statements are inconsistent with some of the loads I used to enjoy shooting out of a Charter Arms Bulldog. Now, I shoot a S&W 696 and barely enjoy shooting loads I would have once considered wimpy out of the Charter, which is weighing almost half as much.
Age brings on many changes.