Sure, the 3 inch slugs have more knockdown power than the 2 3/4 and yes they have a little flatter trajectory. They have a higher muzzle velocity so they about have to.
Now the big question is - does it matter? From my experience - No. None of the full size slugs that I've fired seem to have acceptable accuracy beyond 80 yards (2 3/4 or 3). And if the animal is closer, they all have plenty of power.
What I use the 3" slugs for is practice. With the higher velocity, the trajectory out to 100 yards is simliar to that of the good sabot rounds (Winchester Platinum Tip 400 gr). So when I'm practicing, I always mix in a few of the 3 " just to allow a few more shots while keeping cost reasonable.
For some reason, it doesn't seem to be hard to find 3 " slugs on clearance after deer season ($1 box), so I usually stock up. I guess some don't like them??