I think MGS has held up brilliantly, kind of a glorious simplicity. It has a few caveats, but not really any more than any other classic I can think of, and the fact that it has just that; few, for a fully 3D PSone game is pretty outstanding.
But in terms of the meat and presentation, it's still so great. Great scenario structure, great narrative and voice work, great mood and music, as far as big action/adventures go this and Super Metroid hold up the absolute best, to me.
Part of the testament to it's quality is that Twin Snakes overhauled the superficial bits and still managed to fucking ruin it through subtleties.