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Personally I've played the most of Age of Empires 2 and Age of Mythology.
I've been playing Company of Heroes and stuck my toe into Supreme Commander as well as the Dawn of War games.
Of the Total War games I have played Medieval and Medieval 2, Empire, and Rome (Rome is my favorite).
Everyone says great things about Starcraft 2 but I have yet to jump in.
I LOVE the "Myth: The Fallen Lords" series.
I am a HUGE RTS fan. If you name it very good chance I have played it. It is hard to pick a favorite as most all them bring their own little tweaks that make them better in certain aspects but worse in others.
SC2 is a very very good RTS. Even if you buy it just for single player it has a nice lengthy campaign of 30ish missions, a better than expected story which is strange for an RTS, and then the entire competitive multiplayer aspect. It is not a perfect RTS but it is probably the best all encompassing RTS on the market.
A lesser known but fun unique take on the RTS is Ground Control, and Ground Control 2. They are sort of a cross between Dawn of War and Company of Heroes. The game is about micro instead of macro, their is no base building you gain resources for killing units and controlling territory. With those resources you can call in drop ships with additional units. They are older and actually predate Dawn of War and CoH but you can still get them on GOG.
A similar game to Ground Control but takes place in the late 1980s-early 1990s real world is World in Conflict. Again no base building but instead reinforcements purchased via kills and territory control. A game I very much enjoyed, though same of that is me being a veteran.
If you dont have the expansion for Supreme Commander it is worth the price. Adds in a good number of units and twists. IMO Supreme Commander Forged Alliance is better than Supreme Commander 2. It has a much larger scale and greater variety of units.
Another game to check out is Sins of the Solar Empire, especially if you are looking for a longer more drawn out game. A large map against several AI opponents can easily take over 12 hours (not a 1 sitting game). The game is basically Home World the RTS game.
Then you of course have the Total War games. I think my go to is still Rome, maybe Medieval 2. All of them are enjoyable but these 2 have always stood out to me. very excited about Rome 2 coming out this year.
Since I cant give you 1 or 2 suggestions what I will do is tell you several games to stay away from. I would stay away from Age of Empires 3 and Online. AoE2 is the best in the series and they just went down hill from there. Do not touch Legends of Pegasus. This is more of a 4X game than an RTS but still stay away from it. It is a completely broken POS that never should have been sold. I would also stay away from Theater of War 1&2. These games are not as broken as say Legends of Pegasus, but very rough around the edges. Hard to pick up and not very rewarding. Unless you are really craving a WWII RTS best skipped. Lastly 2 other games that are not terrible but there are better places to spend your money, End War, and Universe at War. If you can get these 2 games for $3-$5 they are worth a few hours of fun, not much more than that.
Well that is my 2 cents.
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Starcraft and Starcraft 2! :D
Living a life of quite desperation, I like to drink when I play games. As such, I stick to the overly simplistic, yet classic, Command & Conquer series. I've spent many all nighters as a youngling playing C&C Red Alert and its successors. As a matter of fact, I am at this very moment waiting of for C&C Tiberium Wars 3 to finish downloading on , GASP, Origin for $16 Micky D's double cheeseburgers. I also enjoy Star Craft 2 and Sins of a Solar Empire when I am sober only. I am giving up playing against real life opponents because I get my ass handed to me so often that I now have raging, huge biceps due to constantly taking delivery of my fleshy ass.
My favorite of all time is Empire Earth but that is only because it takes the near flawless gameplay of Age Of Empires(my favorite RTS series) and includes all of human history.
Well Age of Empires is one of my favorite games of all time so I'll check it out, thanks!
Company of Heroes is pretty good. For me personally I tend to get bored with RTS games fast so I don't play much of them. I also don't have the patience for them. I'd try Shogun 2 if I were you.
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Not sure if it counts as an RTS but I loved Warcraft 3 and it's expansion.
I love Age of Empires 3
Really? I've heard it's not that good.
How does it stack up against 2?
I love the Homeworld and Dawn of War series.
Really wish they would make a modern Homeworld, though the modding community still does a great job of expanding the game and making it prettier.
Gearbox picked up the homeworld series. They are currently making an HD update for both 1 and 2 (and it will come with the original in case they screw it up). After that we may see new entries.
That's incredibly concerning the last two games they picked up. =\
Anno 1404 is my pick.