The biggest difference, other than cosmetics, is the overbored barrel. It's not backbored like the step rib trap barrels, which use relabeled Rem Chokes that take the backboring into account. The Pro-Bore barrel is larger, and uses Pro-Bore chokes that are not interchangeable with Rem Chokes.
From time to time these Pro-Bore barrels have been offered for sale here, and they'll fit any 1100. Unless you want the cosmetics, I'd suggest checking the Buy/Sell section here, and maybe posting a WTB ad.
As far as a 391 goes, I believe they are overpriced for what you are getting. They do break, they still need to be cleaned and cleaning them can be a chore, and on some models the ribs fall off. For the money they cost, I'd expect more. Are they better than the 1100? Yes, but not you're sure paying a lot for that. More important than which gun is better, I'd suggest you try both and see which one feels and handles better for you, and go with that.
I guess I'm in the minority but I think the G3 is one of the best looking 1100's ever, if you could pick one up at a good price you couldn't go wrong. But you will be good with any 1100, the best and most winningest auto shotgun ever built.
The 20 ga. G3 is not over-bored, it is a std. Rem-Choke. The 12 ga. is Pro-Bore. Would be great if it was shimable like the Berettas. At one time, not that long ago Cabelas had them for $659-$699 range cased and all. I think they were closing out the 20 gauge series. I'm a Remmy fan for hunting guns but the G3 is nothing but a glorified 1100 field gun. What does it have over the old 1100 or 11-87? 3" chamber, can only shoot targets with 2 3/4" shells.
I own a 20 ga. 11-87 dealer Premier Edition and love it. Use it some for 5-stand and in the field. Glad I own it. Just not a serious clays gun in my opinion.
Go to a sporting clays course, or a tournament, and except for over and unders you will seldom see anything but Beretta 391's. This year's winner of the Sporting Clays U.S. Open shot a Beretta 391. It was shot by winners of the 2006 and 2008 National Championship.