The only RTS games I ever enjoyed was Battlezone 1&2, Dark Reign 2, Warzone 2100, and Earth 2150 (and the older 2140).
WZ2100 and Earth 2150 in particular because of the whole unit customization thing going on in both games, a bit basic but still it's better than being limited to hardcoded unit types.
Battlezone 1 because it was essentially C&C Red Alert in space, and the combined FPS action sold me. Battlezone 2 was slightly off but still very much enjoyable when you get over the differences, the asymmetric warfare introduced into the game I honestly thought was a welcome edition.
Dark Reign 2, I liked it because not only did it run on the same engine as Battlezone 2, but it was a very straightforward and familiar style RTS to me. Build base buildings, research and unlock the tech tree, harvest resources, and build up a massive attack force. The interesting thing about Dark Reign 2 though, is that Construction Rig's have to "sacrifice" themselves to build the larger buildings, where as smaller ones are built "traditionally" without sacrificing the unit in the process.
I could never stand C&C or Dune II. They're good games but the style of gameplay particularly how bases are constructed just rubbed me off the wrong way. I never played the Warcraft series but Star Craft seemed to have really lame strategy to it, atleast from all the multiplayer games I played. Only thing that kept me playing Star Craft 1 was all the custom scenarios people hacked together on Battle.net
“I am the dragon without a name…”
― Κυνικός Δράκων