IMO:
Alt should just be a "shift" key, to shift between commanding your character, and merc. Like if you have alt pressed, you are controlling the mercs, click with crosshairs-> merc attacks targeted, click with red-outlined-hex -> merc moves to that location.
Later edit: A bit more on this: Alt+right click would remain a menu for advanced commands, like stop all actions, holster weapon, switch weapon, stop all actions etc, and in addition, it would have the low priority move/attack commands aswell. Example: Alt+attack click an enemy is a high priority command. Alt + attack clicking would be another high priority, thus it means target switching. However, alt+right click on secondary opponent, then selecting attack, lower priority means to queue targets, so that when primary is killed, proceed to secondary. Thus high pririty actions that needs quick actions are done via basic controlls with alt pressed, but can still queue with merc menu