Mostly ammo reserves and clip size. I'm sure it varies wildly with each manufacturer but they generally have lower recoil as well. --- Capcom won't see another damn cent from me until Mega Man Legends 3 is released.
Tediore SMGs are, imo, the best because of the reload damage. Huge mag, means high damage. It's basically a full auto smg with an underslung grenade launcher. Dahl's smgs are a mixture between burst assault rifles and smgs. You still have the huge mag and crap accuracy, but zoomed in, the thing shoots 3+ rounds at the same time. If you can accurately aim and hit heads, that's basically instant kill for most things.
Vladof pistols are basically higher damage smgs. My favorite gun in the game is a purple vladof pistol that completely wrecks anything and everything, perfect for my snake eyes ninja zero. Sure you have a smaller mag (and reserve) but if you are doing twice the damage per shot and more accurately, mag size isn't really relevant.
Pistols usually have higher damage than SMGs, SMGs will have higher rates of fire and larger clip sizes though.
Even if you get a pistol that has a fire rate and clip size equal to an SMG, you are able to hold more SMG ammo on you at a time, as pistols like that tend to eat through ammo too fast.
I prefer a good pistol to an SMG, personally.
Im not an expert, but wouldnt higher damage = less bullets needed?
As a personal observation I seem to run out of ammo annoyingly quickly using a full-auto pistol while I've never run out of SMG ammo despite spraying like crazy. It also seems like SMGs are easier to control on full-auto even though the full-auto pistol does thousands more damage. --- You're the stranger, ain'tcha? Are you looking for a nice, clean place to stay? Madam, I had a nice clean place to stay... and I left it, to come here.