I don't know how much of a PITA it is to do such things, but, maybe develop accolades tied to progression content (not AE, not flashback) that grant permanent bonuses that stack or evolve with repetition?
Like say, you plow through the Hollows content when you're supposed to (between 5 and 15); you get a Level 1 Hollows Accolade, that gives every attack a 2% chance to do 2% more damage or something. Now that level 1 is unlocked, if you go through the hollows exemplar'd, you get a level 2 accolade that gives a 4% chance to do 4% more damage. Third time, 6 and 6, and so on up to 10 and 10. Then you move over to Perez and get a 1% ToHit buff (through 5), and in Steel you get a 2% DefBuff, and so on and so on.
If that seems like too much of a bonus, have the accolades earned at low levels only apply in endgame content (i.e. hollows bonus is only active in PI, then maybe a perez bonus that is active in RWZ, and so on) or only when you have a team of 4 or more, or something.
I dunno, just spitballing some ideas that might entice ME to level my alts the old fashioned way, while still leaving AE unharmed.