Command and Conquer 3 isn't my favorite game, but I do like it a whole lot. But #4... Holy shit. Why did you do that EA?!
Of course, I can't not mention Sonic & Knuckles here. Still probably the last Sonic game worth playing. Sure, Sonic Adventure was on the right track, but it needed some improvements to actually make it work and hold up to the test of time (that game is quite awful by today's standards). But, instead of that, it got Sonic Adventure 2, which was the first game to start declining into the mess that Sonic is today. And no, the Advance and Rush series are quite awful too.
It also pains me to say this, but Golden Sun: The Lost Age is one of my favorite games. Then I finally got to play Dark Dawn... It wasn't a bad game by any means, but the story... Holy shit. When I finally beat the game, my thoughts were "Oh gee, I'm glad that I finished that giant fucking sidequest that was 90% of this game. Now I can get back to the main plo- Oh the credits are here. Camelot you son of a *****."