The difference is that Wentz has been telling everybody he doesn't care where he goes. Changing that stance now would reflect poorly on his character, which right now is a significant reason he is being talked about as the number 2 pick. I wouldn't expect him to do that.
Also, if he drops to the late first round that could cost him millions right off the bat and that's a real possibility. Eli was assured of going 4th at the worst.
Oh, and by the way, I think Philip Rivers has done OK in San Diego. For those that don't recall, the Chargers drafted Eli #1 and then traded him for Rivers.