Most of the effort in SC2 went into Balancing, stable Multiplayer + Lobby
and a very advanced Singleplay campaign with cutscenes and such.
(plus Blizzard having the habbit to sack much development work if it does not feel perfect yet)

In an Indy RTS you can simplify that.
Having no or just basic Multiplayer, and textbased intructions
for the missions + only using ingame graphics.

Having an RTS that runs and controls smoothly with nice graphics is managable in an Indy RTS.

There are several Indy RTS out there, wich work quite well.
Only for some reason most look quite ugly.
(probably because RTS are a typical coder-centered domain)
The opposite goes for shooters, wich look good but play like crap.