Of games I actually really loved, I would say Metal Gear Solid is the one for me. The story, music, hell even the visuals are not too bad but good god has the gameplay not aged as well as I had hoped. It was really jarring going from more recent entries and going back to it and thinking "I am so happy it doesn't play like this anymore". I have a sneaking suspicion that if I tried to play Brave Fencer Musashi again, I would get a similar reaction which is why I keep putting it off...

Ocarina of Time would be the other choice but I didn't feel it played that great back in 98 either so whatever.