When I first got into 3 gun last year in April, I would've rated my skills with each of the 3 guns as follows: rifle, pistol, shotgun. It wound up being rifle, shotgun, pistol. Pistol was so far in third place it was embarrassing. So I started shooting USPSA and practicing.
Today I would rate the 3 as follows: rifle, shotgun, pistol lol. While my pistol skills have improved tremendously, I think I will always shoot a long gun better.
I can't say I have a favorite or least favorite to shoot because I enjoy all three. The only one I don't really practice all that much is shotgun. What's weird is that I didn't shoot my shotgun all winter, basically from November thru April and at the very first match of the season, my buddy swore I was lying about not practicing because I was running the shotgun 3X as fast as last year. The only thing I changed was starting a weight lifting program back in February.
But to answer your question, I can't really pick one I don't like because I like them all. If I didn't, I'd shoot something else that didn't involve the one gun I don't like.