Item the First: The betrayal by the US General of TF141. There was absolutely no reason for it, beyond "hey your boss being the big bad is wicked awesome!". Which anyone with any degree of talent in story telling can tell you is a terrible idea. They said he wanted to become a war hero or some other such rubbish when he did it. Guess what? It wouldn't have changed anything whether or not he did kill the squad. He was the CO, he'd get the credit. It made absolutely no sense and was shoehorned in so the writers had something "cool" to work with.
Item the Second: The nuke. Price just got out of the Gulag, wherein he was tortured rather heavily by Ivan for a good long time. He would not, and I repeat not, send a nuke to explode over the capital of his saviors. If anything, it would head straight for Moscow. Yet again, this makes absolutely no sense and it was just shoehorned in so we could do the DC without power level, which I will admit was rather cool taken on its own merits. Unfortunately, that doesn't forgive the complete and utter shittiness of the nuke idea in the first place.
Item the Third: This one is fairly minor and ties into the previous one. When the nuke explode, a shockwave threw the astronaut around and destroyed a couple sattelites. There are no shockwaves in space. There's nothing for the shockwave to travel through, thus it simply does not exist. It's a fairly minor quibble, but it represents most of what was wrong with the story. The writers were trying far too hard to cram in "cool" to create a coherent, logical story.
Item the Fourth, and Final: The airport level. It was an excellent idea, and what got me to buy the game to be perfectly honest, it just wasn't executed anywhere near as well as it could have been. To start, if during the opening briefing they had mentioned you were allowed to shoot the terrorists and still complete the mission, that would've been nice. I would have, but I was under the impression it was the same as the rest of the game where you fail the mission if you shoot your teammates. Other than that, there really wasn't a reason to be there. You are arbitrarily pulled out of Afghanistan and inserted into a terrorist cell made up of random Russians #2-6. There's no explanation for why you're infiltrating, what the CIA thinks their goal is, or even why it was you specifically out of the hundreds of potential recruits in the Rangers that was chosen. It's just "Oh, this guy be bad. You're gonna help him do bad things so we can spy on him." That's an incredibly thin pretext at best.
Almost all of the missions, when taken on their own, were fantastic and a lot of fun. The writing tying them all together, however, was a gigantic pile of rhino dung.
