Hella respect to the foundation a lot of 1998's games left for games to come, but the year really is a poster child for 5th generation as a whole: a lot of games that are better known for their influence, bloated legacy, and ability to tickle nostalgia (though I tread lightly on that last point as I hold certain games dear to me too) more than their gameplay or how they are today.
I have never viewed Ocarina of Time, remake or original when I first played it, as more than a mediocre game. It, like any other 3D Zelda not called Majora's Mask, is thoroughly outclassed in so many ways today, and even then contained a huge amount of idiosyncrasies that added up to an adventure I never enjoyed. I always found more holes in Ocarina of Time than I ever did fun, and even its sequel is really only buoyed from my general disdain towards 3D Zeldas by its sheer weirdness.
I recently replayed Pokémon Red (Blue?), the original, and probably will go to bat for it more than I would other severely flawed games like it as a Pokémon fan, but it's a damn near a bad game at a lot of points. My nostalgic Pokémon choice is Ruby, my favorite overall game is SoulSilver, the best campaign is Black... where does the original fit in? It's still extremely charming at spots, and hell, it beats the pants off the shit we've gotten the last two generations, but it's still a game that desperately needed a remake. It's overall mediocre, but it's a Pokémon romp, and the most simple, shall I even say "pure" Pokémon romp you can get.
I won't even get into MGS1. It's the only MGS I am straight up not a fan of, and any claim to fame it has of being the "simplest" to get or whatever is a knock against its sequels, not a gold medal for it. I played it a few years ago and dropped it because that gameplay is suspect as fuck. It was straight up not enjoyable, and after playing MGS2, I really doubt I'll go back. Chances are if I find a way to get it on my Vita, I'll begrudgingly give it another shot, but it's not ever gonna get its dues from me.
So I'll give it to Grim Fandango. I think it's a good game that absolutely peaks in Year 2, tanks very, very hard in Year 3, and doesn't recover very well after. But Rubacava is legitimately one of the most memorable sections of gaming I've ever played, and the overall conceit of its story and the sheer amount of charm lets me overlook, to an extent, the almost asinine puzzle design. I would kill for the game to be as good as Year 2 on a constant basis, but that's how the cookie crumbled. So the best game I played in 1998 was a good one, which is not great for a year. Maybe I'll play Xenogears soon. Who knows.