How would you win? First to three or five or seven captures? I like this idea.
Generally in CTF, there is a "jail" were players need to go if captured or tagged. But in RTS, it might just be easier to make another unit instead of capturing it, so I propose that if you kill a unit, the cost of the unit is passed on somehow to the team who killed the unit. This makes winning battles very important, and gives you a huge advantage after doing so.
I think that it would be good if buildings were indestructible, but on the flip side, it would also be good to make a limit to the number which could be built.
Another possibility would be that there are only certain units which can capture the flag. They have a specific command "capture", just like a Swordsman has an attack command. These "capturers" could be killed, which brings military back into the picture. It would be wise to bring military along to guard the capturer ("Guard" is even a command in GAE! Brilliant!), and battles would certainly ensue over this.
I like Vaylon's (welcome to the forums, by the way) idea of flag locations, but another possibility would be that we can choose where to hide the flag, as long as it fits certain parameters (enough space around the spot, etc. Maybe locations should be tagged in the map editor, making flag placement less guesswork ingame. I want to make sure that there is a little hide-and-seek game going on to actually find the map, because that is a part of the fun!
A final note I have to offer is that it may be wise to make capturers a later-game unit, so some dominance must be asserted before any capturing can go on.