I think part of the issue is that some people only have X amount of time to play the game, and in their mind, would they rather play a character with only a few powers and struggle against some "lesser" enemies, or sit in an AFK farm and do other stuff, so they can play what is, in their opinion, a "fully fleshed-out" character. Game knowledge be damned - they'd rather struggle with learning their end-game character than slog through yet another "kill all" or "find the glowie" mission in a confusing cave map. The only ways to get people to behave in a desired way is to punish them for deviating from the "correct" way to play or to reward them for adhering to said "correct" playstyle.
Some possible solutions, IMHO, would be:
1. Grant players a significant amount of reward merits for completing non-flashback story arc completions, (while sub-50).
2. Grant players significant amount of XP for completing said sub-50 story arcs, (again while being sub-50).
3. Related to 1 & 2 above, implement a system whereby one can still follow the chain of contacts and storyarcs, even if they have outleveled them, and still have those missions provide level appropriate enemies.
4. Dramatically improve how mission objectives are tracked & handled. For instance, if a glowie passes through your field of vision, mark it on the map and/or provide visual/directional indicators, beyond just the audio ones. Give hostages +1000000000 perception, or whatever amount would be necessary, so they can still see the player through stealth/hide/etc. No more stealth kill-all's! Respect a player's time and don't pad out missions with things like portals generate endless enemies - either have them grant XP and be endless, or have them be limited; If it can kill you, it should grant XP.