In Empire Earth you potentially go from the stone age to the future age (with around 15 other ages in between) which required you to match up units to defeat each other. For the ancient to medieval example: shock troops defeat ranged but are defeated by piercing, who are in turn vulnerable to ranged. In the imperial era's and up to WW1, you get different ranged units who fulfil the same balance. In ship combat, there were again 3 different types of ship, and they all balanced. WW1 onwards, its riflemen, tanks, and other units who make up the balance until (get this) you get mecha's in the future. Aircraft come into the equation as well after WW1.
I can't remember exactly how that worked, but it certainly required some forethought into how you composed your forces, particularly on offense. Like in Age of Empires, you needed some foresight to get through defences. Got siege weapons? Great, if you can defend them. Otherwise your soldiers are almost hilariously poorly equipped to deal with walls, causing one damage per swing as the archers and artillery behind the walls rain sharp pointy death down to the point where even the shock troops are going to be dying like animals. (or whatever unit is good against extreme range units in the era you're in.) and thats not even discussing the turrets (hope you have long-ranged siege units, otherwise you'd best be in a position to say "we have reserves" because your attacking force is going to be brutalised even with close range siege equipment.)
To add to all this, instead of technology counting for all units, you could upgrade each unit individually. Your shock troops been in a few unlucky encounters with piercing units? Upgrade their piercing armour. Waves of enemy siege weapons threatening to overwhelm the defences before you can even reach them with your defenders? Take your fastest unit, give it a few speed increases. Turrets too weak? You can either improve their attack or their health. Brings specialisation to new heights, but note there are a limited number of upgrades you can use on each unit type.
I'm not usually a fan of RTS's, but I have to admit, I enjoyed that game, and it definitely involves more thought than most. You will get utterly ruined if you just build one type of apparently powerful unit.
EDIT: I've noticed a lot of people talking about Rome: Total war. Thats not really an RTS in the more traditional sense. It is supposed to be a turn-based/RTS mix. However, you build all your units during the turn-based phase, and can't build any more once out on the field in RT. So it isn't really comparable to your traditional RTS "build your legions of doom and send them out to crush all blocking your dominance of the screen" gameplay type. It is the closest you will get to running a real battle though, you will feel like a general, especially if you manage to pull off victory when outclassed. I would certainly recommend it. I'd also recommend Medieval II. I'm not in a position to recommend Empire: total war, having never played it due to not having the computer for it (my damn PC can't even run the Sims 3.)