The gameplay mechanisms and controls are unusual and surprising for a RTS. I was a little bit lost about what I have to do, but once I got it it was really fun!
Maybe you should think about giving more information at start for the player, like a small tutorial.
About the flag system, I feel it's very promising if it was more polished. For example, it didn't work so well to drag the flags (often considered just like a click), so I ended up not using this feature at all.