I think the biggest area where the wait times is a problem is in some of the Assault promotion quests. This is only a wait until next game day (so a maximum of 1 hour instead of 1 day), but it can still be VERY frustrating. I'm thinking here especially of Promotion: Sergeant Major, Promotion: Second Lieutenant, and Promotion: First Lietenant. These quests require you to play some puzzle minigames and wait until next Vanadiel day if you fail. The minigames are a bit of a brain teaser and can be tough to figure out, but they'd be a lot better if you could just retry instantly in the event of failure. As it is now, people just force a disconnect during the minigame to reset so that they won't have to wait.
A lot of people are talking about a wait between cutscenes in mission lines. I think that's a good idea, but maybe not as critical because it's a thing you will do once in your life and never again. It can and often is a problem when you're doing missions with a static group and someone forgets to do cutscenes until the last minute and no matter how hard he tries can't catch up with you in time for a planned run at the BCNM fight for that mission.