First, the hardest level in the game, the Abbatoir, has you fighting off a wave of enemies who have come to kill the hostages. They're led by Vyasheslav Grinko, and the mission automatically ends when he dies. You can A)Fight them off traditionally and get overwhelmed, B)Set some traps and reprogram turrets, then fight them off, a way in which it is possible to win, but difficult, or C) set traps, sneak to the front, and snipe Grink, difficult to time (as you have to move fast enough that the hostages don't die, but slow enough that you aren't found), but by far the most effective.
The last mission of the game, the Georgian Presidential Palace, is much less infuriating, but just as climactic. Taking the story elements out of it, you end up finding the Big Bad himself, Kombayn Nikoladze, standing conveniently by the safe you have to force him to open. Once you do, a Georgian Spec Ops team comes down, takes Nikoladze, and a few hold you at gunpoint. When they begin to ask questions, Lambert informs Sam that he's arranging a blackout. When that happens, Sam is able to disappear (although you can fight if you really want to, but they're tough). Once you get out of that room, you need to be invisible. You need to get to a balcony with a good vantage point into Nikoladze's office, and if you're spotted...well, he won't be in his office when you get to the vantage point, and you fail. Anyway, you need to snipe him, then escape to the waiting Osprey, but it's much easier said than done.