It's been a while since I saw it, but from what I remember the original airing was fairly intelligently scrambled. You have a spine of episodes that consist of the original light novel, which occur in the same order they did in that book. This introduces the characters and the main plot, and ends in a climax that has to be at the end.

You then have a series of one-shot stories from the books (and one original episode contributed by the creator of Full Metal Panic!) that get scattered throughout, as there wasn't enough content for a full season, and it would be weird to have the climax occur mid-season.