I agree. Starcraft-style games are all about resource management. Personally, I find that the C&C line are less this way than the -craft line, but it's still strongly that way, especially in the initial set up.
Dune was, indeed, the first RTS of this sort (that I'm aware of, at least).
I've never played Civ, but I very much enjoy Civ2. Great game. If only it had been originally released as multiplayer. My brothers and I learned a lot from it, though. (for example, it was the first place I'd ever heard of Adam Smith) =þ
You'd probably like the upcoming Warhammer RTS (Mark of Chaos). It's got an interface that might be somewhat like the Total War series, but from what I've read the emphasis is going to be much more on tactics and battle, rather than on resource management (thank goodness).
"Dark Omen", a previous Warhammer RTS was loads of fun, and was ALL about strategy (seeing as you didn't get much say over your army one way or the other).