VII and IX. They are the best. VI is good but the game slow down really bad in the middle/end. There are people who don't like VII genuinely and then everyone else who hates it because "boo cloud is emo I've only ever seen commercials for Advent Children". VIII is the only of them that I would actually call bad. The story isn't great, most of the characters aren't developed, the magic/battle system is super grindy.
As much as I love the MGS series, there are a lot of plot points that really suck. Liquid's Arm in 2 was pretty awful, but I got over it quickly. What I'll never get over is the further explanation given in 4. I really, really dislike what 4 did to the MGS universe. The series took place in world only slightly more supernatural than our own, and I loved that aspect of the series. In 4, they explained away the supernatural with nanomachines, and it took away a lot of the magic.
Other than the arm thing, you still had all Psycho Mantis's stuff from MGS. His damn ghost appeared in MGS4. Ghost-ghost. And you always have The Sorrow. No nanomachines back then. I just wish Vamp was some kind of android...
Final boss of Crysis. It's just a big ship thing that you have to fire that nuclear gun at. It would have been more fun just to kill a bunch of the tripod-squid-aliens. "Oh fuck they're going to sink the ship if we don't stop them! Nomad we need you to stop them in time!"
I didn't hear anyone say this but I figure the xenomorph at the end of the movie is a baby queen. We know how normal ones are born, but now how queens are born. It looks more like a queen than a worker/drone anyway.