Chapel was stronger and faster at achieving density. It becomes a clog in the later rounds, while Pauper doesn't. It rated extremely high to be sure.
Turn 5 Pauper looks stronger, for example, Chapel might have a 10 card 10$ breakout (1$ exactly per card), while Pauper might have 9 cards worth 10$ (1.1) But here's the thing, to get denser you HAVE to buy another Pauper. That slows you down a buy, while Chapel surges ahead. Think about it, if the goal is to remove all 3 Estates and up to 5 Copper, that requires 4 purchases of Pauper to achieve.
In the later rounds Chapel is a pain, but the set has cards to deal with that (numerous cards set cards "aside"). So in this set, the Chapel is more prolific. You know what's actually a superb thing to do is to buy the Pauper, in hopes that you can actually trash your Chapel. Get the Chapel to narrow your deck to the point where drawing the Pauper and the Chapel together is very likely, then Pauper the Chapel to have both cards eliminated. In games where density is more important than Curse-elimination, it's a really nice move that worked out really well in a game we played.
I think you might be right in that Pauper is a tad over-powered. It certainly rated that way. It would have rated even higher if it were not for the fact a lot of times, both players purchased it. In games where one player purchased it and the other didn't, it's win rate was staggering. So it is a very strong card. I think in most instances, Chapel is better, but let's face it Chapel shouldn't cost 2$, you could make an argument Chapel is worth 4$. So Pauper is probably worth more than 2$ as well.
I think I am going to live with that though, as the card enables fast games and launches you forward in turns 4-7, which produces an exciting game. If I were more honest with myself, I'd cost the card at 3$.
However, I really value your feedback, if you feel the set would be stronger with Pauper's cost adjusted or its abilities nerfed, I will consider it. All the advice I've gotten on this forum has been excellent, I'd be a fool not to listen to it.