Command & Conquer 4: Tiberian Twilight, hands down, IMO.
EA completely dismantled the tech tree and base building. I've played C&C since I was 7 years old, and they completely destroyed the basic building premise, which the series HELPED TO DEFINE IN RTSs. I couldn't even finish the game. I ended up reading how it ended on a wiki. I honestly don't know why they changed it. They kept C&C 3 and its expansion the same, and I liked them a lot. Kane's Wrath (the expansion to C&C 3) was probably the best RTS port to a console I've ever played (as far as adapting the controls went), and I loved the story. I played Command & Conquer 4, and after the third level, I just couldn't take it anymore. A bit of my childhood died that day.