I have experienced that with my .45 as well, if you have a range that lets you rent weapons try it out. You will find that the .45 is more of a push instead of a snap as far as recoil.
There has been talk about the DoD going back to a .45, but in all honesty I do not see it happening. MARSOC runs .45 because we regularly run our weapons suppressed, to get all the suppression you can, you need a subsonic ammo. .45 ball is already subsonic, so we do not have a loss in lethality. Where as with 9mm at supersonic you still get the supersonic snap after the projectile leaves the barrel.
But we do not really run suppressors to be stealthy. We do it more for command and control purposes, and because it reduces recoil. Makes it easier to communicate with each other. Suppressors do not sound like they do in the movies.
IF the DoD does change rounds for pistol, I would be willing to bet that they go with a .40.
Here is a suppressed M4
YouTube - Suppressed M4
If you listen carefully you will hear the supersonic crack (the pinging sound is because he is shooting at a steel target). You could run subsonic ammo, but you would loose a lot of lethality, and a lot of range.
5.56 gets its lethality because all spitzer type projectile (any projectile that is longer than it is wide) will yaw in the target, because of the high muzzle velocity you get core separation when talking about 5.56. The wound channel is actually larger for 5.56x45 than 7.62x39 or 7.62x51 (NATO) because of this.
M855 ball in 5.56
7.62x39 Russian lead core coper jacket.
Now if the 5.56 hits the target slower than 2400 fps then it will not fragment. That is why subsonic in 5.56 is not a good thing.