I have never run a "real" MyBB forum, but I ran a number of test sites many years ago as I basically used it to learn php before moving onto using vbulletin.
Can't stand sidebars on MyBB at all, it looks too much on there...like could few some space up on it.
The most important thing about MyBB are actually two things,ha ... it's FREE and it's pretty good (as free script) for spam fight, generally. Much better than SMF etc ... It is simple and it's Template system is easy to understand. But the biggest lack is plugin system. It is good system, but when it comes to deactivating and removing plugins ... you don't have an option that will just remove all the Plugin's files, you must do it your self?! Most People can not deal with it, so eventually many, many unnecessary files remains in your MyBB installation. But generally I believe it is one of the best Free Forum Software ever.
Some premium themes won't work with MyAlerts and other mods. But to the developer's credit, sometimes they will fix the situation for free.