Ahh, Civilization and I believe Alpha Centuri aren't RTS - RTS is REAL TIME Strategy, whilst Civ and Alpha are turned based 4X strategy. I'd almost say the Total War series fits this category, just with real time tactical battles, though its an odd case so I'm not really sure.
Now, thanks to you not distinguishing between the two I will give recommendations for both
RTS:
-Age of Mythology. Is a must, especially with the Titans expansion. Yeah, its old now, but its still fun, and forming a Titan slaughtering wall is waaay too much fun.
-Warcraft 3. You've played Starcraft, Warcraft is Blizzard's other RTS. Slower paced, more emphasis on micromanaging the units as opposed to the primarily macro focused Starcraft, and with a ton of custom maps that allow it to transform into a million games for you to try. Also, make sure you get it with The Frozen Throne expansion. Its not quite the same without it.
-Rise of Legends. Fun and entertaining, though starting to show its age. Campaign that switches between RTS battles and turn based research and movement throughout 3 stages. 3 unique races with many different special units and spells, and all round an interesting and fun RTS to play.
-Rise of Nations + Thrones and Patriots. Really starting to show its age now, but a very fun RTS spanning from the stone age through to the present. Has a grand campaign similar to Rise of Legends, but played on a map of Earth trying to conquer the world.
4X:
-Galactic Civilizations 2. One of the great 4X games, alongside the Civilization series, and very fun to play once you get all its expansions. Campaign starts off easy but quickly becomes brutal, but the normal matches are still fun and scale well. You are able to design your own custom ships using parts that you can then deploy in game, which can lead to many fun moments involving your fleet of Imperial Star Destroyers attacking an enemies fleet of Battleships, even though the game has nothing to do with Star Wars. A bit dated, but still fun.
-Fall From Heaven 2. If you've played Civilization 4 with the "Beyond the Sword" expansion [Which you should if you haven't, it adds a lot to vanilla Civ IV], then you may remember the Fall From Heaven: Age of Ice mod that came with it. Now, take that, and turn it into an entire 4X game on the level of Civ IV. That is FFH2, with a lot of new races, units and tactics that you'll have to utilise to win. Random events are fun and sometimes challenging, and there are a lot of ways to win, some dependent on your race. The armageddon counter is interesting and something you have to keep in mind whilst playing the game, and there are a lot of things you can do in it. It is basically a whole new game, but a free mod if you have BTS.