Despite my other issues with Panera, they remain my go-to bagel shop. The wife loves them. I'm finding that if you time things right, you can get what you're looking for. Once in a while they will run out of good bagels earlier than they should (imho), but that's business, I guess.
I do enjoy toasting an Asiago bagel and putting some butter on it. Plain and simple, but delish!
Staff is friendly and the place is clean. If you *need* bagels - call ahead or be early.