I'll have to go with Twin Snakes. Though REmake was certainly commendable on technical merit alone, it still isn't, nor originally was, as good as MGS, imo. MGS has aged far better as well, and I don't mean graphically, but specifically control-wise and in just overall design. REmake still suffers from horrible control and item management, and though the puzzles are generally well thought-out, the task you're actually accomplishing is almost always completely idiotic, and making the entire game revolve around going from one of these tasks to the next can get very tedious.
That said, I still haven't gotten to Zero Mission, though I'm sure that will be very good as well.
