I would vote for the 4 inch version. While you do lose on the sight radius that can be easily addressed by adding a reflex sight such as the J Point to the gun. BTW, most long distance handgunners have now gone to using Optics, because they provide such a big improvement for sighting at long ranges. Sight radius for a reflex sight at 50 yards is 50 yards, so it's difficult to match that by shooting with irons.
The downside of the longer barrel is that they are heavy, expecially the fully lugged barrel on the 686. I have a 6 1/2 inch 610 and a 6 inch fully lugged 617 and am quite familiar with the effect of that muzzle mass, it gets tiring to hold after a while and when fatique sets in, accuracy goes out the window due to shake. In addition, during rapid fire drills, the longer barrels have a strongly negative effect on group size. The problem is that during rapid fire that extra mass in the barrel makes it much more difficult to return to the target quickly because of all that inertia. You either swing past the target and have to come back to Point of Aim, shoot with the gun moving, or slow down your firing rate. The best grouping that I can manage with my 610 at 30 feet at a 1/2 second split is a pretty poor 7 inches. Compare that to the 3 inch group I can shoot with my 4 inch tapered barrel 67 at the same distance and split time and you can easily see the effect of trying to move all that mass quickly.
IMO, the only advantage for the longer barrels is if you intend to use the gun for Hunting. That extra 2 inches in the barrel will provide a bit more velocity and will extend the effective range somewhat. How much, I really can't say, I limit my hunting range to my group size relative to what I am hunting. Quite simply, I won't take a shot at a distance where I know I can't shoot well enough to insure a clean kill, which for me isn't long enough that velocity concerns are that important.
Bottomline, the shorter barrel is a much better choice for Defense or Gaming. In addition, it's a lot easier to carry a revolver with a shorter barrel. BTW, even with the 4 inch barrel the 686 is a touch muzzle heavy, enough that it will have some effect in rapid fire. Good news is that it won't matter from a Defensive standpoint, I can still shoot by 620 into 4 inches at 30 feet and the 620 is very nearly as muzzle heavy as the 686. However it noticeably less nimble in the hand as my older tapered barrel 67 which has the sweetest balance of any revolver I own. If you want a revolver for Bowling Pin matches, IMO the best choice you can make today is a 3 inch 686 or 610 and equip it with a J Point Reflex. I can't afford one at this point, but someday I'll have the funds for one. Hopefully, I'll get lucky and find a 3 inch 610, which is a personal grail gun for me.