1. Add complications and variables. Players don't mind having to use a strategy. As a rule, half the FATEs should not be able to be completed with only 1 class, much less one person. You can give the baddies any level of variables. That would stop the pure thoughtless-fest. For example a boss that multiplied when you used aoe or fates that required actions like putting out burning buildings complete with rescuing and healing people. At the end of the day, a rpg should be about more than how much damage you can dish/take.
2. Create a hard mode. All those fates where the guy stands there and waits for someone to open the FATE? Yeah. Plenty of opportunity to make FATEs specifically for the level 50s who want extra challenge (they show show on the map as a different color) instead of having a bunch of fully decked pcs completely negate the new guys who are using the FATEs to level. On its own, level sync is not a challenge it's a replay.
3. FATE Actions. FATEs are supposed to be people coming to together, but has anyone made a friend through a FATE? (Not a FATE party, an actual FATE). Do people work together during a FATE or is it mindless? I can't be the only person still upset they never made anything in this game as cool at the THM ARC fire arrow combo they had in the 1.0 cut-scene. Allow different combinations to create different effects.