When I delete an email, a pop up gives me a chance to compact folders now, or remind me later. This is a minor annoyance and can probably use a fix. I do want to compact folders, but not while I'm in the middle of reading and deleting my email. I have my compact filter set to 2000 MB alrady.
How about using whatever trigger is used to, instead of popping up the small window, do a delay and open the popup when it's more convenient and useful, like when I delete my trash or go to close the program? Maybe, as soon as mail download is completed before we get to work. It wouldn't deal with later deletes, but they'd just stack up to the next time.