The "your player is dead" trick was over-used to the point of becoming laughable
I laugh every time someone says this, since it only happens once that isn't optional. It only happens twice if you count the astronaut, which fills the same purpose as Al-Fulani in the first game. Watching Allen buy the farm is completely optional.
I've heard lots of people say the story was confusing? What, exactly, was confusing about it?
Makarov sets the U.S. up as the fall guys for a thousand dead civvies in Moscow. Russians get pissed, attacks the U.S. Gen. Shepard takes a hand-picked taskforce to find and kill Makarov. To find Makarov, they track down his arms-dealer. From him, they find who Makarov hates behind reason, and go to spring from jail to lure him out. To GET to the guy, they disable a gigantic SAM site on an oil rig, which also happens to help the U.S. attack a little bit of Russia, as well. When they find the guy, it's Price. Price then spits in Shepards face and EMPs Washington to get the U.S. and Russia to stop killing each other (I admit I don't see the logic behind that, but it isn't hard to follow, story-wise). Shepard and friends then gear up to take down Makarov by attacking his safehouses. Player successfully takes safehouse, steals Makarovs operations playbook and all that. Shepard kills player to tie up loose ends, since "history is written by the victor," and he wants history to be as he says it is. Soap and Price get shot at by everyone, escape with Nikolai in a C-130. Soap and Price go after Shepard. They kill him. Game ends.
Really, it isn't that hard if you actually listen to what's happening.