Being a huge RTS fan, StarCraft II, IMO, has been the best RTS around and will continue to be for a few years at least, and before SCII it was Brood War and Warcraft III. Other game developers need to put in the effort to polish their RTS games like Blizzard does, but I guess RTS market is deemed too small and too risky. Total Annihilation was a great game but it's too bad Cavedog went under and Chris Taylor couldn't recreate a game as great as TA. I've played most of the games mentioned here, although for Warzone 2100 I only played MP once or twice. The playerbase doesn't last and there's no continued support from developers unlike Blizz so it's hard if not impossible to get back to playing these games.
SupCom: I used to play mostly UEF but then switched to Cybran for a bit before quitting. The campaign was lackluster and the multiplayer got boring pretty fast for me. I think FA had decent balance but Cybran were probably a bit OP. Had high hopes for that game, as a huge TA fan. Really disappointed.
Battle for Middle Earth II was a fun game, besides probably having the longest name for a game ever, the campaign was kind of decent. Again, MP was inbalanced... I mostly played as Elves, I remember them being pretty OP compared to some of the other races. I remember putting the Eagles to good use. I think eventually there was a fan made balance patch to fix a lot of the issues.
Also, the players who are good at one strategy game will be usually good at another, it mostly comes down to getting the build orders right, scouting, reacting, etc... having a good APM really matters. When it comes to high level play, it's an "APM clickfest" no matter whether you're playing a "true RTS" or StarCraft.
Also, there is a community made TA inspired Spring RTS game. Don't play it for the graphics, it's got a balanced and routinely updated TA mod. I played on their multiplayer lobby for a few years.