Since I can't decide on one...
Half-life- The ending is far weaker than the rest of the game and revolves around a mechanic obstructively introduced at the last minute. While ambiguous stories can certainly be good, it only really works when it serves to emphasis the main conflict. Half-life, on the other hand, simply leaves everything ultimately unresolved, but incredibly undeveloped.
Silent Hill 2- The story is wonderful, but the "video game sounds" can occasionally detract from the atmosphere. While it possible contains one of the most emotionally charged scenes I've ever seen in a video game, the voice acting is horrendous to point that I'm hesitant to actually show it to anyone. Even on the highest combat difficulty, the game is way too easy, provides way too much ammo, and the monsters can all be easily outran, so it never has a super big sense of danger save a few boss fights. While it's creepy, it never really has the kind of moments in the first game that me stop playing and remind myself that it's only a game.
Fallout- The game presents seeming endless possibilities for completion, but because of the ability of super mutants anyone with better equipment than you to insta-murder you, it means that you only have a handful of actual options for completing the game. While most people would criticize the time limit as being against the spirit of the game, I'd argue that it was a wasted opportunity. It sort of touched on the idea of thorough vs. expedient instead of good vs. evil, but it gave players so much time that running out of it never becomes enough of an issue. Perhaps they could of solved this by allowing the player to fail the main quest without getting a game over, but they didn't. Also, while the game does allow the player to side with the antagonist, it causes a non-standard game over and it's only real build up is poorly done.
Myth: The fallen lords- The narrative structure is interesting, but the game never really goes anywhere with it. There isn't enough dramatic progression to make the main story interesting and the narrator is too underdeveloped to have any character development. There aren't any note worthy twist or turns, nor is there enough foreshadowing to make the narrow victory satisfying. Stuff sort of just happens and people say dramatic things while the narrator describes how hopeless everything is. Furthermore, some of the difficulties present in the game such as the weather or terrain often make success seem like more of a matter of luck than it makes players think of different solutions. Because the game forces you along a path where several events can happen which can only be prevented by chance, the game often comes across more as trial-and-error than strategy. It's also worth noting that the physics engine could have been used to far more interesting effect than it was. Sure, it occasionally effected the odd grenade or arrow, but the fact that people can be killed by the weapons of dead units just screams to be exploited through gameplay.
Deus Ex- Ah yes, even the pinnacle of player choice and immersive simulation has flaws. People walk funny. The player eventually got too powerful to be challenged by anything. The story based player choices had very little consequence to the gameplay. The game stopped caring about the difference between dead and incapacitated after the second mission. There was never enough stuff to buy, but when you did have the chance, stuff would likely cost you all the money you had for a small benefit. Some of the augmentations would never be all that useful unless fully up graded, but never would be because there weren't enough upgrade modules later in the game. Rifles were practically useless without skill investments, but the heavy weapons could be used untrained with almost as much effectiveness. Hacking was literally pressing a button and you only needed a single level of it to make use of 90% of what it was good for. A silenced sniper rifle was so effective and had so much ammo that there was never really any reason to use anything else. With master lever rifles, it also became 100% accurate and could kill anything in one shot that wasn't a bot. Stealth became increasingly useless later in game as it placed the player against enemies that couldn't be snuck past or incapacitated with a prod. Bodies couldn't be dragged unless you had the inventory space to hold all of their worthless stuff. People would become un-alerted again too easy and (save one mission), there were absolutely no consequences for going full rambo and then hiding. The entire game takes place at night, but you character always wears sunglasses...
They have more design decisions that other might call flaws, but they actually enhance the games. With all of that said, I absolutely love them and few things can really compare to them.