Xenoblade- To me the perfect balance of a story being complex with a lot of twist and turns and room for the gamer to figure stuff out without drifting into the convoluted and wacky. Also balances MMO like style with a large open world and tons of optional grindy sidequests but with a compelling main storyline.
Pokemon- They're cute and the battle system is great. Games are mostly interchangeable to me.
Skies of Arcadia- Mainly because of the reasons mentioned by the OP, but I think they're selling the story short. Essentially it's a tale of two naive children being dumped into the world, one seeing the best humanity has to offer and one seeing the worst.
Tales of Symphonia- Classical RPG tale of chosen hero needing to find x macguffins to save the world from destruction. But what it does it does incredibly well.
Paper Mario 2- Best of the Mario RPGs. Great script that is constantly amusing, and does an amazing job of giving you various scenarios to keep things fresh like becoming a wrestling star and solving a train mystery.
