The airboat sequences are definitely weak, but they're still worlds better than the vehicle sections in most games, and I found the payoff of killing the gunship to be quite satisfying. I think my favorite sequence is the Nova Prospekt sequence, beginning with the approach up the beach and ending with the delayed teleport back to Kleiner's lab. The pacing/level design is fantastic. The flow from beach into ruined prison into retrofitted prison into fully converted combine facility is seamless, and extremely engrossing. Some might complain about the turret defense sequences, but I quite enjoy them, and if you think they're too hard you are bad at game.
Breen's rants about the failure of the combine forces up to that point are great as well. They serve to inform the player about the state of the world, give some hints on the back story, the structure of the combine and Gordon's whereabouts during the missing time between games, as well as stroke your ego a little bit.
I almost feel like playing through it again.
