My favorite RTS is actually an MLS (Multi-Level Strategy).
Total War (all). It started with humble beginnings when Shogun came. But it has gradually improved in many facets. No other strategy game (or RTS) has evolved as much in 10 years as the Total War franchise. It is the ultimate realization of well paced gamer focus, as well as displaying a realistic passage of time, and providing the gamer with a complex of varying challenges. The well paced gamer focus comes from each of the areas:
The turnbased focuses on the strategic element of economics, macroscopic war planning, logistics, role playing the family members. If you send your son to stay near a brothel in Empire TW, he will most likely build up negative character traits such as hedonism and alcoholism.
The realtime focuses on the tactical elements of battle; morale, terrain, relative weaknesses, feints, ambushes, ammunition etc.
The ways in which Total War has genuinely evolved has been very satisfying. It's had its flaws. There were some really bad historians working on Rome TW, but the Total Conversion "Europa Barbarorum" fixed that. The AI was flawed as well, and still is. The most recent additions to the game mechanics have been naval battles and a very basic form of logistics/supply. I'm sure the logistics will evolve even further.
My favorite regular RTS is Total Annihilation and Supreme Commander. Supreme Commander 2 was horrid. For that huge disappointment I blame Steve Bauman and some other folks.
Supreme Commander 1 (and Forged Alliance stand alone expansion) has shown many meaningful evolutions in game mechanics of the classic RTS genre. The "Zoom on cursor" function, which has long been normal in 3D graphics applications like 3D Studio Max and Maya. Epic scale, nice pacing. Economic model requiring little micromanagement rather than having to babysit some sheep-like peasants or harvesters. And there are even further streamlining of functions to REDUCE micromanagement. Such as the "Ferry flight" function. Fantastic music by Jeremy Soule.
I find it disappointing when journalists praise a gaming franchise for having changed little. Usually we're supposed to praise pioneering and advancement in our culture. With Starcraft 2 this seems like everyone will praise someone for a stagnant franchise even after 14 years development.
The common knee-jerk response is usually
"If it ain't broke, don't fix it"
That's the mantra of stagnation. Well, I think if you wait till you're old and frail before you evolve, you're going to get extinct.
I appreciate how it's geared toward the eSports market. I also appreciate how polished, balanced and bug-free it is. But I'm almost sure that the same game would've never been given half the praise it got if its name and content wasn't Starcraft 2. The mass media (media owners, editors and journalists) operate on corporate expectations and the power of suggestion. To give Starcraft 2 scores of up to "100" (which I've seen on some metacritics) is simply obscene, because it's essentially the same game as it was back in 1998, with updated graphics and new units. But I'm thinking maybe Starcraft 2 and R.U.S.E. can be classified as eSports RTS. Though I genuinely liked RUSE.