Other than cooling it will be a pain is there any other reason not to do this?
Nope. It will probably taste even better the next day. Just reheat gently, and wait until serving time to top it with croutons/cheese (if you're serving it the traditional way.)
Bet that's what a restaurant does! You can probably make the soup days in advance (even freeze it for a month), then reheat and assemble to bake. Cool it partially covered to lessen evaporation.
I do this frequently. I either make the soup and then add the croutons and cheese when reheating it, or I caramelize the onions ahead of time and then reheat them with the liquid portion of the soup.
Thanks to everyone for their answers. I really like the idea of getting the onions out of the way in advance and then making the soup from that point the next day.
It also means you can make extra onions and you only have to freeze the leftover onions and not the soup, thus saving freezer space!
I caramelize my onions in the crock pot on low for at least 12 hours or so until they're nice and brown - you can do longer if you want. Then add the stock and cook as normal. This would facilitate doing the actual soup the next day. I don't have a good broiler so I toast bread slices and cheese in the oven the top the soup bowls, instead of doing the bowls under the broiler.