That's why its a plot-twist. Like Indy going over the cliff in The Last Crusade. You think he's dead, and then surprise he isn't. You should be savvy enough with storytelling by now that to know that you can never take it for granted that someone is dead. Upon replaying that scene, the medic trying to revive Price looks more inconclusive than anything, especially since we don't get to see Gaz and Griggs (two characters who are definitively dead) getting the same treatment.
2) The battle was easily over. At the end a loyalist Mi-28 comes in and annihilates the rest of the ultra-nationalists in the area around the bridge. At that time, CoD was in a more realistic setting, and the ultra-nationalists were a small faction, not a group that had taken over Russia, hence the likelihood of their helicopters being shot down is nil
The Ultranationalists were hardly a small group. Remember all that military hardware they had? Every mission you play as the SAS has you fighting them. Hell, they even managed to secure their own missile silos. And they'd been fighting Russia for years, even during Ghillies in the Mist they'd been at it for a while, and were that the SAS considered it prudent to assassinate their leader. I'd say its safer to say that the Ultranationalist movement was closer to a full-scale civil war, which is how it turned out in MW2.
3) No, no, TF141 knows who Makarov is, of course, why doesn't Russia? I suppose Russia didn't want to look at the CCTV footage, so they gave it to TF141, they had better things to do, like attacking some unrelated country. Who's the more likely mastermind behind a shooting in an airport. The well-known terrorist holding a gun and shooting, or America? What did America have to gain from slaughtering Russian civvies?
Again, Ultranationlist warmongers. Russia probably did see it was Makarov leading the attack, but so what? He had a CIA agent with him. That can easily be spun as "USA working with terrorists to bring down Russia" (Ironically, this turns out to be partially true). And yes, Russia could easily tell Allen is a CIA agent. They do have their own intelligence agencies. Or, hell, Shepard could have the info "accidentally" leaked.
4) No, it's a plothole. If you think launching a nuclear missile is as easy as typing in a city you don't like and pressing enter, you've got it very wrong. Besides which, it takes two people turning different keys to arm a nuke. Even getting into the sub and down to the launch room would take more than the two minutes it took Price to launch the nuke. Saying "it's awesome" doesn't make it good storytelling, it just furthers the idea that CoD fans are retards obsessed with big explosions and over-the-top BS.
I said Price was awesome, not the act, but that doesn't change the fact that we didn't see what happened in the sub. For all we know, the missiles were already primed and ready to launch and Price just let it happen, with small adjustments so they'd explode high in the stratosphere rather than at a more dangerous altitude. You are worrying an implausible scenario in a game which is founded on the idea of implausible scenarios. Its a techno-thriller, that's how these things work. We could counter each other's logic all day, but since we have no idea what went on in the sub it's pointless. I agree, if they'd cut to a scene of Price effortlessly hacking into the Russian missile network I'd be skeptical, but they didn't.
5) SAM's are usually small-ish, big enough to be truck mounted (hence no need to be connected to a network). You just wait for a plane to enter within range, and BOOM! It's gone. There are also anti-air tanks that are specifically designed for taking down aircraft with high-power rounds. And don't forget about Stinger's and other portable launchers that are actually featured in the game.
It takes a lot of time to mobilize that kind of stuff. And again, National Guard and Army reserve. Double again, most of our good stuff was in Unspecifiedistan. You have to remember that the Russian attack was a complete surprise, and they hit in a very wide swathe. You can't just poof a bunch of stinger launchers and SAM trucks exactly where you need them at a moment's notice.
6) Doesn't change the fact that assaulting the US in an all out invasion is suicide, thus very stupid. Any country that spends trillions annually on war is serious business.
Which is why the attack doesn't work

Go America! I get the feeling the attack on Washington was supposed to be a quick "in and out" attack. Decapitate America's ruling bodies, shatter its morale, then move in the heavy stuff. That's why it seems to be all paratroopers and light vehicles for the most part. MW3 will likely show the "real" invasion.
7) I mostly mean Canada and the UN. Do you honestly think America's geographically closest ally would stand by idly as Russian jets screamed overhead? Likely not. We aren't as big an army as the US, not even close, but we'd still help out. And the UN would throw a fit at Russia. Not sure how much it'd actually do, but it'd still happen.
You have to remember that the entire game happens over the course of a week. And its scope is limited to D.C. and part of Virginia, which is probably outside the circle of immediate logistical support from Canada. Who says they aren't fighting? We don't know. Ditto with the U.N. But as MW3 is going to take place at least partially in Europe, we'll definitely get to see what they've been up to. My guess: Russia decided to take a swing at them too.
8) Makarov isn't crazy, he's a genius. Either way, imagine if in real life, a Russian terrorist who had worked for the FSB blew up the Empire State Building. First, you'd have Americans crying about how it's the worst tragedy in human history, after which... Well, likely nothing. Russia's oil to military strength ratio isn't high enough to risk an invasion over.
You also have to take into account that their leader was recently murdered by a joint American/British operation. But remember, the Ultranationalists aren't operating on the same wavelength as your average person. They WANT to fight, and have been spoiling for one since they took over Russia. As for Makarov, the guy is a terrorist. Kills people for fun and profit. There is some crazy going on in there. And regardless, I doubt they'd be privvy to the various internal politics of Makarov's gang. Maybe Makarov and Allen didn't get along? Maybe Allen was wounded and Makarov considered him a liability. Maybe Makarov shot him because he was revealed to be a secret CIA agent who was manipulating him to help start a war with Russia? Plenty of reasons, but so long as the UNATS got a hold of a dead CIA agent holding a smoking gun that killed Russian civvies, they really couldn't care less.
Also, you're wrong. Thinking about the story will expose it's flaws, it's not thinking about that will let you accept it as credible. Just because something is fiction doesn't mean it has to make absolutely no sense. It's okay for a story to be sensible, in fact, I'd ever go as far as to say it's a plus. Any good sci-fi story can still seem plausible, even though there might be laser guns, FTL travel, whatever. Since MW2 is, well, modern warfare, it'd be nice to have a story that is believable. I wouldn't care quite as much, if CoD4 hadn't been wonderfully written game. Well, as wonderfully written as an FPS game can be expected to be. Try to find one plot hole in CoD4 and maybe you can nitpick on one or two things. But MW2 is utter crap, story-wise.
Fine, plot-hole for MW1. Price nails Zakhaev with a .50 cal round, blows his arm clean off. The shock alone would have killed a normal man, the huge blood loss would have killed anyone else soon after. There were no medical facilities, and he was in the middle of nowhere. How did he survive? IMO, this is even more egregious than Price surviving MW1. Its no more of a plot-hole, but there you go. Even MW1 chose story over believability when it had to.