The passive skills available for Pistols counter to Shotgonne are different.
The Shotgonne is focussed on short range area of effect damage, and the pistols are more of a long range option.
The Pistol can benefit from the Long Range Mastery passive skill that increase damage by % and the range in meters.
The Long Range Mastery passive also buff damage and range on Bows, Crossbows and Wands.
There is also a Akimbo passive skill that increase damage by a % and the chance of performing a Execute where both pistols are fired simultaneously.
For the Shotgonne you have the Shotgonne Mastery passive that gives a % chance to stun for 2 seconds increase the knockback and has a % chance of blinding.
You might also want to consider the skills you use since some does a % of your weapon damage and others does a flat damage.
Personally I stick with 2x1 pistols and Rune Vault for a kiting build.
You could also consider a Bow, if you like the long range passive along with a weapon damage based skill like the Rapid Fire.