I'm not sure Ponder would want to be Archchancellor even if he could. It's pretty clear that he already runs the place and the university would grind to a halt without him - and he knows that. I think that's enough for him. All the power without the responsibility.
But the university is a very different place than it was in the early books. It changed pretty much when Ridcully turned up. Which incidentally was around the same time that Ponder turned up as well.
“Men never commit evil so fully and joyfully as when they do it for religious convictions.” – Blaise Pascal