A flatter trajectory makes it easier to hit objects at undetermined ranges since one needn't estimate the range as carefully, but once you dial in a range, you'll find that the issue isn't one of accuracy but one of range estimation. (i.e. once you get the range estimation problem out of the way, the fact that the rounds get there slower won't have a significant effect on the ability to make little groups until you get to the point that wind becomes a major contributor).
Rifling exposure is a non-starter. As long as there's enough rifling to get the bullet spinning at the proper rate (and an inch or two is all it takes) then more rifling exposure does nothing to improve accuracy.
The bottom line is that barrel length is really not a contributor to accuracy. In fact, all things being equal, a shorter barrel will actually tend to shoot more accurately because it's stiffer. It's not uncommon to see "bloop tubes" added to iron sighted match rifles--these tubes allow the actual rifled part of the barrel to be short while the sight radius is kept long or perhaps extended.
The PRACTICAL reasons that rifles tend to be more accurate than pistols have to do with:
1. Increased stability due to a shoulder stock and better control of the firearm.
2. Increased sight radius.
3. Fewer moving parts in the barrel/chamber/sight system. (No revolving chambers as in a revolver, sights tend to be mounted directly to the barrel rather than to a separate slide, barrel tends to be fixed to the receiver as opposed to moving separately, etc.)