I like Shining Force as an RPG of it's time because it did something different with the multi-party system that Final Fantasy had and that Zelda didn't have in any way, you could even argue that it has better graphics but in the end, it owes a lot to the other 2 games and doesn't have the strength of character or story to have stood the test of time like they did.
I'm voting for Ico because it's simply one of a kind. Plenty of games have levels where you have to protect and guard an NPC but (off the top of my head) none of them created an entire game out of the idea. There's certainly no other game that comes as close to being defined a work of art, a near silent storyline that somehow manages to be more engaging than 99% of bloated cinematic heavy games out today. That's not to mention the epic scale of the castle which is just one massive puzzle and a truly impressive sight. It's only one generation old but I can't wait for the Ico/SotC HD release later this year.