It depends on the caliber. Obviously a harder hitting caliber or one with more viable SD ammo is more desirable...to a degree.
I'd pick a lower capacity 9mm over a comparable .380. Yes the 9mm is going to be a bit snappier, but the performance of the ammo should outweigh that as long as I can keep my first one or two shots on target.
That said, I would still choose the 9mm over something in .40 simply because the .40 tends to have (for me) more perceived recoil than the 9mm compared to the .380 when you get it down to single stack carry pistols.
When you start getting into .45, I feel that you lose too much capacity and shootability when you start going smaller than your 4" barrels. Even though the .45 isn't as punishing as the .40, I think then I would take a .40 over a .45 if it allowed another 2 shots per magazine.
Of course, all of this being framed in a smaller concealed carry hypothetical. Outside of CCW, it's all out the window. I wouldn't really want to carry a full size .380 for any reason short of a range toy. I slightly prefer a .40 over the 9mm when I'm grabbing a heavy hitting full size for outdoor/woods carry. I probably shoot a 7 shot 1911 better than any 9mm, but I still tend to gravitate toward full size 9mm simply because it holds twice the ammunition of the 1911 and weighs about the same.
Now let me muddle it up completely. Day to day, I generally carry either an LCP stoked with hardball or an SP101 without a reload
At the end of the day, I like how packable the LCP is despite it not being a powerhouse, and I shoot .357 very well out of a heavy snubbie. Even with the decreased capacity. the chunky little Ruger tends to win out over other pistols.