Personally, I don't think you can classify one ending as being all-round better than the other. Different people like different things, and of course, it also depends on the superstars involved. If it's Kurt Angle vs. Chris Jericho, I'm hoping for a submission, but if it's John Cena vs. Batista, it should by all rights be a pinfall. There are very few superstars who can go into a match and you don't know whether they'll win by pinfall or submission. Kurt Angle was really the only man who could keep you guessing, as he had the Ankle Lock and the Angle Slam. They have given John Cena the STFU, btu he mostly seems to end with the FU still (I think JBL is the only man to suffer the indignity of tapping out to John Cena this year, at Backlash), and they tried it with Brock Lesnar for a short while, with that Brocklock thing, but you mainly expected it to be the F-5 finishing off.
Right, that's the all-round answer out of the way, now for personal opinion. Solely for me, I think submission is more dramatic of a way to end a match. You don't know whether they'll tap or reach the ropes, and they can keep it going for so long, with the guy suffering the hold trying desperatly to reach the ropes, and his opponent dragging him back at the last moment. They can also use it to make it seem more real, so to speak, with the looks of pain you always see "etched across the face" of the superstar locked into the hold. The only thing that ruins the drama of a submission is that stupid over-the-top thing that has happened with Khali, and more recently Undertaker, the bleeding from the mouth skit. It's unnecessary, and it looks stupid. However, on the whole, I think submissions are more dramatic, and also give a straightforward ending. A pinfall can happen at any time with something as simple as a roll-up, but a wrestler being made to tap out, that's definetive. He gave up the match, it's over.