Mine has to be Dark Reign: The Future of War. It came out around the same time as Starcraft and Command and Conquer so it was pretty well ignored by most RTS gamers. The one element that grabbed my attention was the AI of your units. You could send them off to scout, harass and seek and destroy but then control variables like health tolerance, independence and pursuit range. So I'd set a bunch of air units to harass and place them on a low health tolerance, they'd scout the map for me, shoot enemy units until they ran out of ammo or took 50% damage, return to base, repair and bomb up, then rinse and repeat. This allowed me to spend more time building up a main force to attack rather than having to micromanage a ton of units.
Whoops, a bit long there, but I haven't seen another RTS do it since and it was such a good idea.
Whoops, a bit long there, but I haven't seen another RTS do it since and it was such a good idea.