Don't end up here: you have 3-4 followers who are 98+, one or more of which is level 100. Most of your new missions are now level 100, and most of those take 2-3 followers. This is an easy place to get to, but it really drags you down because the rest of your 97-and-under crew can't contribute or earn XP, you have level-100 mission generation that is going to waste, and your lower-level-mission generation is now poor.
How to avoid this: always be giving your highest-level followers a break. NOT pushing them up a level keeps your mission generation down where more of the rest of your team can use it. If you're benching at 98, don't let one level until enough of your team is 97+. (Ideally all of your rares/epics, and any green with a unique counter or Epic Mount.)
ALSO, you have to restrain yourself from gaining new followers in any way until you've researched their level and determined it won't raise your current max. This is how I blew it today, I bought the blue Kang from the Frostwolf rep vendor without realizing he'd be 100.
I'm going to find out if deactivating him lowers my quest generation again, but I have to get to 21 followers first. If anyone knows for sure, please reply. I will update post with my own findings.
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Update: Got to 21/20, deactivated my one lvl100, and all 10 or so new quests that have come in since then have been below 100. Whew!
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Update 11/19: Blizzard just hotfixed mission generation so that the levels of missions you get better reflects the levels of followers you have active. So there shouldn't be a need to hold back / deactivate your highest level ones anymore.