I'm not sure how others will respond, but I use different gauges and different barrel lengths for different species, as well as different chokes and loads. I should tell you that I only shoot over-and-unders and side-by-sides with fixed chokes. I don't own an autoloader, although I do think about it now and then. Here's what I shoot...
Quail, Doves, Snipe, Pheasant, Grouse & Huns:
20 gauge, Mod/IC or Mod/Mod or Full/Mod, 26" barrels
Ducks & Geese:
12 gauge, Full/Mod or Full/Full, 28" barrels
The shotshell load varies with the species.
If you're looking for an all around gun to use for both doves and ducks, it seems to me the primary issue to address is what kind of shooting you'll be doing the most of...if it's waterfowl I'd go 28" and if it's doves I'd probably go 26". Then you should know what size shotshell the gun will chamber and whether or not it has screw-in chokes. You'd probably do well with a 12 gauge that has choke tubes and that will chamber up to a 3" magnum shell. That way, you can use the more open chokes (Mod/IC or Mod/Mod) and 2-3/4" shells with a light load for doves, and then go up to tighter chokes (Full/Mod or Full/Full) and 3" shells with heavier loads for ducks.
There are a lot of experienced hunters in RTF, so I'm confident you'll get a variety of opinions. Good luck!