Since I generally go into games with no expectations, I'm rarely disappointed, but there are a couple of games that come to mind:
I found Red Faction 2 to be a major disappointment from the first one, largely because the setting had been entirely changed, and some other things I can't really recall right now, as it's been a while since I played it.
Starting my second play through of Bioshock, only starting to wonder after a couple of hours as to why I liked it in the first place. The more I started to think about it, the closer I came to the conclusion that many parts of the gameplay was very poorly designed and executed.

Many gaming magazines built it up for me and I went through that game disappointed. The Big Daddies were incredibly stupid and east to kill, I never died during the game, and the last boss was like a puzzle you see on the kids menu at Gringos. Fuckin easy....
I got bored of it fast.

Me too. Only it's not a shrink wrapped copy. It's a barely-covered-the-postage-cheap eBay copy that I grabbed. Still, it's like new and won't be seeing any real use until something is done about its unfinished state.
It's not actually the collision detection but rather that you're 'rolling a miss'. The game works on a somewhat more traditional role playing model that makes bugger all sense when converted into 3D.
The curse of episodic gaming.
I find that, with the 1.7 patch, it's actually pretty stable now. Then again it could also be down to switching to a Geforce GTX card. Both happened around the same time. Either way, it's a lot more stable than it was.

I know that it just infuriated me I spent 5 hours getting to that level for 10 days only to STILL be hitting like I was at level 1...

This better be the last one or I'm going Left4Dead on their asses.

Combat sucked in Morrowind. But at least you could mod the hell out of it and there were tons of quality mods too.
You mean you're going to be neglected in favour of that which was supposed to support you?

I actually had no crashing problems right out of the box with the game, but as there came more patches and DLCs the game has started to CTD out its ass. The peculiar thing, is that I never had any problems when I only had custom mods. Really annoying, and very strange.

I can't say I had the same luck with the launch version. It definitely crashed a lot. But it was with the 1.5 patch they really screwed up. That was utterly terrible. They seem to have finally got it right now. Although I haven't tried taking Pitt equipment back into the wastes. That was one significant problem they might not have fixed.
*midway main quest spoilers*
One odd bug I encountered with 1.7 was talking to 'Dad' after he died. Using third person mode you're able to talk to him. He starts out talking while he's laying on the floor then gets up and talks about how I've got a cloud hanging over me (my alignment, I presume), while leaning forward looking a bit... undead. Then after talking he stumbles around and dies again. Very strange.

You mean I wasn't the only one who played that game? Shame it was just about button mashing else it could have been a fun, albeit mindless, action game.

C&C Generals - man, this shit doesn't deserve the C&C name.
FEAR 1+2 - my friend was still telling me about it (ZOMG atmosphere! ZOMG horror! EPIC GAME!!!!), so I tried it out......I turned it off after 1 hour and then deleted it immediately. Pathetic.
Red Alert 3 - I still regret that I bought it. At least I got the fur cap as a bonus from preorder.
Oblivion - dumbed down Morrowind with poor story. Nuff said.

I liked (but didn't love) Bioshock the first time, but after you've been through it and know what's around those corners and what's going to happen, you start to notice that the gameplay and combat is actually pretty bad.

Though i think that illustrates an interesting point. If the game "experience" was good enough that you enjoyed it the first time through... is it fair to pick it apart because its weak points become more apparent over time?
As for morrowind... the way the hit calculation works means you're never gonna have a 100% chance to hit... unless maybe the enemy is frozen or asleep. Same goes for almost every other RPG doesn't it?
I thought of another though, and it ISN'T due to high expectations this time...
Xenon 2:
Fought my way all through that game (which was darn hard at that age/experience level). And you get a tv-style fade to small white dot in the center of the screen. WTF??

I'd have to say the ending of Prey was disappointing. You really think we're ever going to see Prey 2? Pfft. ;)

I think the first time, at least in my case, I was baffled by the very setting, which sort of managed to overshadow this. I also played on a lower difficulty, where some of the flaws were not as apparent, and since I pretty much had the plot and the backstory out of the way, I could concentrate a lot more on the gameplay, which made the faults a lot more apparent.

being super excited about Oblivion coming out. didn't work out for me. Who the hell thought a hundred carbon copy oblivion gates would be fun? Plus, I went full stealth character, and by the end I had a REALLY hard time killing anything because my combat skills weren't that great and bow and arrow didn't really do that much damage. I really ended up having to use sneak and arrow kills for EVERYTHING, which gets old.
Star Control 3. ugh. Loved #2.
Buying Dawn of War 2 and realizing that I'm really not that into RTS's anymore. I used to love C&C and Red Alert.
Starlancer + stupid insta kill beam weapon. Uninstalled.