Ummm... Ocarina of Time is just as easy as Wind Waker. I blazed through Ocarina of Time without dying once on my first try, and I didn't find nearly all the hearts. Zelda games haven't been hard since the NES. In fact, Ocarina of Time was probably the biggest disappointment I've ever had in videogaming, it's not even 1/2 as good as A Link to the Past or Link's Awakening. Personally, I think Wind Waker is better. And Metroid Prime is definitely better than anything for the N64.
My vote for best game post SNES... Castlevania: Symphony of the Night. But then again, most of my favorite games are post SNES...
And I feel your complaint against Metal Gear Solid, I've said it many times. While the games may be overrated, they are still a blast to play. I have Metal Gear Solid 2: Substance, which has plenty of gameplay on the other hand. The Snake's Tales, Alternate Missions, and VR Missions add at least a good 80 hours of gameplay, if not more. I'm 10% of the way through with the VR Missions and Alternate Missions and I've played about 12 hours so far. And they are a blast to play, except for some of the weapon missions for VR... GRRRR...
But the Sneaking and Variety VR Missions and Alternate Missions... definitely awesome.
Also, speaking of the Seiken Densetsu series (Secret of Mana was Seiken Densetsu 2), find a rom for Seiken Densetsu 3 as it is a MUCH better game. There was a PSX Seiken Densetsu game, it was 4... called Legend of Mana. It was ludicriously easy, had a very patchwork style of gameplay, and was quite boring... but the art and music were absolutely astonishing. Probably the best artwork (not graphics, but artwork) for the PSX, and definitely some of the best music. If you go into it expecting a beautiful aesthetic experience with mediocre gameplay, you won't be disappointed. I couldn't finish the game myself, once the novelty of the art faded, I couldn't even think of picking up the game again. It was such a shitty game...