I've only played MGS 1, 2 and 4, and I played them in that order. MGS 3 is in the postal system somewhere on the way here though, along with the rest of the HD collection.
"The original and the best" (well, the original solid game), is how I'm voting, as with most things. Gameplay-wise it certainly wasn't very sophisticated and it seems that every subsequent game improved things in that area, but it was good enough.
More importantly, MGS 1 told the best story of the three I've played, and it kept things relatively simple. MGS 2's story was ridiculously convoluted, and MGS 4 just tried to say too much. As a nice, tight, simple package, MGS 1 was fantastic.