I used to like building massive bases on RTS games too, sort of like a sim base thing. I did this on C&C1, RA1, TS, Earth 2150 (awesome for base building), Starcraft (need custom map skills but best for base building). I also played settlers but only to settlers III which was fun for base building but mines run out and trees eventually stop growing to maturity (bug i guess) and my city just halts. Anyways i still have all these huge bases in a folder so i go back to them and mess around from time to time. Earth 2150 was decent because the base could come ready built from the map editor, the AI's construction truck could be kept behind a wall, letting it out would start the action. Starcraft has custom triggers that trigger a massive attack on my base, amongst other stuff, theres turrets that can be activated/deactivated, doors, a sort of invisible firestorm wall, and two AI's on the map who present a constant threat but they attack eachother mostly rather than me which is fine.
Recent RTS games dont seem to use grid based structure placement which kinda buggers things up for my perfect bases, i tried to make a huge base in c&c generals and it just sucked, went back to my TS base to breed viceroids instead. So starcraft II might be fun if the map editor is similar to starcraft's one, or maybe earth 2150 if you havent tried that.