Peyton Manning has more experience, and better leadership and decision making skills. He's more intelligent than Eli as well in his choices. However, Peyton injured his knee, and had to get surgery, and it affected his mobility in and out of the pocket. Also, Peyton can be really funny in his antics. I love how he always makes changes to the play, and then just barely gets it off in time.
Eli is younger, and has better physical fitness than Peyton. He can move a bit better, but that small bit may be all you need. Eli also has more fire and drive that Peyton.
You can't really judge which one is better. You have to take into account their teams and playing styles as well.