Squad/micro-strategy mechanics in fps games. Commanding npcs to do specific things in the middle of a gunfight isn’t fun. Bonus points if the npc ai gets in your way when you’re not fighting as well.

What games are you specifically thinking of here? The comment brings to mind the Brothers In Arms series, which was built entirely around controlling your troops and it was great.

I'm wondering if the problem is more of an issue with controlling NPCs being kind of half baked into an existing game than the concept itself.