MGS.1 has the best collection of bosses, easily.
And Shadow Moses Island is easily the best setting.
2 is great, but it lacks in these categories
Yeah, the mechanical changes introduced for MGS2 are great - and holdups are the single funnest mechanic in the series - but there's a bunch of stupid bullshit that came along with it.
MGS1 is almost unplayably ugly to my modern tastes - and, sidenote, I wish Square had remade Vagrant Story instead of FF7 as another 'stuck on PS1' title that is also almost unplayably ugly - so Twin Snakes still sort of holding up but with the improved mechanics from MGS2 is why I'd choose that to replay. It looks
good even in places when emulated.
The GC controller is pretty great for certain types of titles, but MGS isn't one of them, so another notch in an emulated versions belt.
I'm also glad they didn't radically redesign the environment; its still Shadow Moses. It was a good environment to set a game in.
Complaints about difficulty or cutscene changes... eh.
MGS is an easy game anyway, adding optional mechanics that make it easier isn't destroying it anymore than those new mario games having invincibility powerups if you keep dying on the same level do, because you can always just not use them. It is pretty fucking funny taking down revolver ocelot in like, 10 seconds after all his showboating though. The OG MGS was always full on anime too - even outside of Psycho Mantis fourth wall fuckery, you've got Grey Fox ridiculous bullet dodging nonsense and a guy who cut off all his extremities to play dress up.