I'm currently trying out the various free SDKs out there (Cryengine3, UDK, Source) however all of them are mainly designed for FPS games. I was wondering if there are other AAA 3D engine SDKs that are aimed towards RTS games?
I believe what you are looking for is the Broodwar API (BWAPI). Although not an official SDK, it pretty much allows you to do anything in Starcraft: Brood War.
It even has a yearly competition supported by Blizzard.
PS If you decide to use it, don't forget to check out two very important extensions:
The simple fact is this: RTS games are not as popular as FPS games. And people, particularly people who make "free" stuff, tend to make what is popular (or what is easy, hence the thousands of Minecraft clones). That's what attracts multiple developers to a project, and multiple developers is pretty much the only way to make a "AAA" engine of any kind.
Because of that, you have to pretty much take what you can get with RTS game engines. The best are going to cost money, and you're not going to get anything even close to the quality of, say, the StarCraft II engine without paying for it.