One I will always recommend is AI War: Fleet Command. It's one of the best RTS games to be released in recent years, but most people never end up playing because they can't look past the 2D graphics. They miss out, but it probably doesn't matter much because if they're that shallow this game will likely go over their heads anyway.
The basic premise is that AI machines have taken over the galaxy and basically wiped out almost all of humanity. The AI is now in hibernation, and you're all that's left to oppose it. The key being that you should try and keep the AI unaware of you for as long as possible, because the more you attack them the more aware they get and the bigger threat they pose.
It really is one of the best strategy games money can buy, because it actually requires a lot of thought on the player's part instead of him just memorizing build orders. If you start taking planets over too early, you risk the AI starting a full-scale invasion again and wiping you out while you're still weak. What is amazing about it is that the AI is also very adaptive and learns from you. If you try a certain strategy once, and then try it again the AI would likely have come up with a plan to counter it the second time. Similarly, the AI scouts out your planets and checks for weak spots in your defense and strategy and then takes advantage of that to hit you hard. If you've got a lot of defensive structures around one wormhole, but leave another less defended, the AI might circle around the galaxy and try to enter your planet from the other wormhole.
It's really an amazing game and it's highly unlikely that you'll win your first few scenarios, because the key to playing is to build up your forces so that by the time the AI realises what a threat you pose and they start waking up their overlords, it's too late for them. Very few games give you the satisfaction that you get when finally beating an AI in AI War.




