This is heresy, but...
I've always felt that one effective way to address this problem is to increase the damage differential between single-target and AoEs. Whether this would involve nerfing AoEs or buffing single-target attacks (and enemy hit points, thus effectively nerfing AoEs), I can't speculate. Maybe just dramatically increasing the END cost or cooldown of AoEs would be sufficient. In the genre, AoEs often are depicted as requiring ultimate effort from the protagonist and leaving them drained afterward,
A very large part, if not the entire part, of the problem of teams blowing through crowds is due to being able to effect, and kill, crowds with a few clicks and subsequently not much animation time. And yet the superhero movies and comics we love feature predominantly single-target attacks for most of their dramatic effect. AoEs exist, but are mostly used to dispose of minor threats ("trash") before the plot moves on to duel with the big bad. Crowds are terrifying UNLESS you have AoEs, in which case they're exciting targets but trivial threats. In real life, of course, being outnumbered was dangerous...at least until the era of weapons of mass destruction, explosive shells and machine guns.
If most of the work of bringing down mobs had to be single-target in nature, crowd fights would take longer and be scarier, but individual defeats of each bad guy would remain satisfying. Debuffs and buffs would matter more.
I realize AoE is ingrained in the playerbase at this point. I don't expect my idea to be adopted, but it does address the key problem and it would improve the experience.