OP, due to the length of my fingers (they are long, I take L/XL gloves) and the shape of my natural grip vs the shape of the Glock trigger guard, my middle finger took a beating when shooting my G21 or G30s. I had a similar problem with the trigger guard of my .44 Ruger SBH. I could shoot all of them well enough, but they hurt, as in actually bruised the second knuckle of my middle finger.
So, I have to disagree with your premise. Some guns are just not going to feel good.
At the other extreme, I have a female PD detective friend who is a tough little firecracker type. Fitness buff, and a martial arts instructor. She's tough, but she is small and has small hands. She can't get a decent grip on her department's issued G22 and G27, so she is allowed to carry a Beretta .380, which she can actually grip while getting her trigger finger into proper position.
Another friend of mine had an epiphany about finding a gun that fits her hand properly, based on her experience with her first motorcycle. She and her husband had picked a bike based on price, brand reputation, mpg, handling... but she had problems with dropping the bike when stopped. Quite frankly, the frame and seat were too tall for her, so she could never get the balls of both feet comfortably on the ground. She traded for a Honda Shadow, with a seat several inches lower, and the problem went away since she can firmly plant her feet when stopped on the new bike.
She then applied that concept to issues she was having with her Beretta 92 (which she and her husband had picked out, too), and is now looking for a J-frame or possibly a snubby K-frame, since she knows from shooting mine that she can get a proper grip on both of those.
Grip size, shape, length; trigger reach; those are going to be factors that practice may never really overcome.