I think this one kind of goes without saying, but I'm not going to spoilertag my post. This is an 'endings' thread, so... durr. Spoilers. But!
Halo 2 - Now, I know that Halo is in no way a game about it's story (although the story-lovers of us, the ones who like stories even in story light games (can I get a Mega Man Hola?) don't care and still sorta like Halo) but that was such a bullshit anticlimax. HOLY SHIT EXPLOSIONS! ALIEN WARP HOLES! FUCKIN' CHIEF ON THE COVENANT DOHICKY. "Finish the fight" Credits. ... Uh... What!?
Metal Gear Solid 2 - I am a huge fan of the MGS series, but I hate 2, and I only like 4, where it should have been amazing (because the gameplay is, but the story portion is... fucking weak) But 2's ending was such a colossal clusterfuck. If video game endings that are convoluted and stupid were ancient gods, MGS2 would be the 16th Colossus. SOLID SNAKE SIMULATOR SYSTEM FOR SOCIOTAL SANITY NANOMACHINES WHITE HOUSE ROBOT PATRIOTS I NEED SCISSORS CHILD SOLDIERS ANGSTANGSTANGSTANGST PREGNANT JACK ROSE TITANIC RAIDEN WE HAVE TO FIGHT NOW. I hate 2 in general. It's controls are by far worse than any other game in the series (MGS1 definitely included) The bait and switch was weak, and the story took what was an espionage with-a-twinge-of-woowoo and turned it into a full bore ROBOTS AND NANOMACHINES! Basically waving away Psychomantis, any of the other supernatural shit in it. And then, when 3 was more of a James Bond film than whatever 2 was (Black Hawk Down meets Wristcutters?), they explain Ocelot is the son of The Sorrow, essentially explaining how Ocelot could channel Liquid, only to turn around and NANOMACHINE it. Fuck 2. It put a pall on my favorite series.
MGS4 - This one sort of teeters on so awesome, it's almost fucking horrible. Like, I dig Big Boss coming back. I do. But then he had to go to explaining shit that got stacked up from 2. The patriots, nanomachines, Liquid Ocelot (Something that could have just as easily been 'Liquid possessed Ocelot, but then saw that Ocelot was trying to fuck the Patriots, and was like, Shibby, let's go.' Just... Ugh. This is a good death, Right? For this series, it deserved better.
Fallout 3 - Now, I know this was retconned by the DLCs, but, Fallout 3's original ending was freaking miserable. Especially if you were a heroic character. What is the big pay off for being a paragon in a world coated in evil? Oh. You die. You get fucking microwaved. And if you send your buddy in so SHE can be microwaved? Nope. Game over. Everyone borking dies. Oh, hey, what about the seventeen foot mutant who is sympathetic to your goals, and is totally rad resistant. To the point that you would have to put him in a microwave till he died of starvation? HE could go do i-...what? Destiny? Oh. Right. Yeah. Ever notice how destiny is pretty much synonymous with too-stupid-to-live? It's right next to twoo wuv.
Minecraft - Face it. You stopped playing every world you ever stopped playing because you dug through a wall with four stacks of diamond, ten iron, six gold and your army of pickaxes dwindling, only to drink lava. Shitty end, no?