This game had a few innovations that were carried over into the rest of the series, such as the radar that shows enemies, and the various alert statusses.
It was a bit irritating that I had to go through three end bosses (Metal Gear D, Grey Fox and Big Boss), and none of the bosses are really that hard. The AI of the enemies isn't that good.
What is also irritating is that you spend lots of time wandering around the three buildings. You frequently have to get from one building to the next and back again. That's just not exciting, and indeed rather irritating. The puzzles are pretty convuluted too, in such a way that it will be very hard to get through the game without a walkthrough at some points.
I had thought that this game would expand more on the story, but that is hardly the case. There are some conversations that support a theory of millenia and me that Big Boss was trying to die by Snake's hands at the end of the game -- in order to pass on his legacy. (Though Grey Fox does pass on the Fox name to Solid Snake -- Solid Snake is "the best", whatever that means.)
On to replay Metal Gear Solid!
ETA: Slow Beef's Strategy Guide for the game is hilarious.