Compacting folders is something I hope that they fix. I tell Thunderbird to download/sync all accounts and immediately it prompts me to compact and if I let it, it will only fail with an error because it's still in the middle of doing what I just asked it to. A little more intelligence in when it prompts for compacting would be nice.
Better yet, they could do a better job handling it automatically so I don't need it to ask me.