Then I'd say Yoshi's Island. The game just feels so flawless to me. Main points:
Perfect level design-Filled with bonus challenges, stuff to collect, and deep devotion and care. Also, I believe this was the first game to have individual scores for each level, which adds a sense of accomplishment for doing so.
An amazing soundtrack- Very different tunes and very fitting for each level. And Baby Bowser's theme just yells out epic. Bowser has a lot of great themes, but this is definitely the best one. And that's saying something.
Story- Fairly simple, but that's the beauty of it: it's the essence of childhood. I still nearly jerk a tear every time I beat the game and see that "Heroes are Born!" screen. Also, this was the first game to have both diverse dialogue and direct dialogue from the enemy's point of view, both provided by Kamek. Even though he's the bad guy, you feel for him. And he has a lot of witty things to say as well. Baby Bowser's great too, thanks to his little desire in anything but riding a gween donkey.
Characters-Besides Kamek, all of the other characters are great too. This was the first Mario game to give you a lot of people who actually were nice and wanted to help you...Poochy, Muddy Buddy, Goony Birds...even the Chomp Rock sort of is like a helper. And plus you could really abuse the enemies in creative ways, my favorite of which are stealing the Grinders' melons and hitching a ride on the Goombas.
Charm-This is the game's strongest point. Little subtle details everywhere make the game a treat. Kill the little bud of Naval Pirahna and you get a special message from Kamek. And of course there's the TOP SECRET TELL NO ONE message which isn't even that hard to find. And making Cactus Jack sad by eating his Needlenose...little details like that which show a great amount of love.
Item inventory-A big plus. With a game like this, 1-ups become meaningless. That's why an item inventory is essential to add diversity. Getting rid of it was one of Yoshi's Island DS's biggest mistakes.
Length-Actually quite a long game. Not much to say about that, but it's definitely great.
Control-This is seriously one of the most fluid games I've ever played. You can do anything. Projectiles that go anywhere you want, slow speed to very fast, multiple jumps to just barely make it back...great all around.
So that's why it's my favorite.