The original MGS, for me, is the best overall. Superb pacing - you're always on the way somewhere, with a clear goal in mind, and a new set of obstacles to overcome; a sharp contrast to the two subsequent games, where there's a lot of idleness or repetition.

Best fights - unique boss fights, rather than sporadic duels with shallow bosses. The Cobra fights in MGS3, like the Cobras themselves, feel like they were included simply for the sake of having 'boss fights' throughout the game. In MGS1, however, each major battle is relevant to the plot in some major way.

Great characters - every FOXHOUND member has an important role in the plot, rather than being tacked-on for dramatic purposes. Very well developed, even those with little screen-time, like Mantis and Wolf.

Significantly, I feel that MGS is less... well, 'self-important' that its successors. Probably because the latter games were made with the knowledge that they were part of a gaming legend. The original MGS, while carrying on the legacy of the old 16(?)-bit games, was in a format that was untested, so it wasn't guaranteed phenomenal success from the outset. I think it benefited as a result.

I have major issues with how the series discusses World War Two, but the first game was by far the most reasonable. By the time you reach MGS3, the game would have you believe that Japan's involvement in the war was thus: 'they were an utterly peaceful nation, doing nothing except enjoying blissful pacifism until some evil Americans started dropping nuclear bombs on them for no reason, which was the single worst atrocity in human history'. The first game is far less propagandistic in this regard, though that remains my biggest grip with the series as a whole.

Basically, MGS1 wins for originality, creative challenges, a heavily involved plot and cast, and simply setting the standard that its successors have striven to emulate.