Has anyone mentioned the element of Generosity? Spike's always doing things for Twilight, because he's a generous and helpful dragon, and Rarity also has that trait. So other than a physical attraction to her *ahem* "plot jewels"... they just have similar characteristics that work well together? Both their faults/opposites involve greed as well (Spike's birthday episode and the whole thing with Rarity and Tom.)
I am surprised Spike didn't have a crush on Twilight actually. Would love to see him find a sweet dragonette ^^
Rarity is supposed to be the most beautiful of the mane six, so I would imagine it is as simple as that and would certainly make sense that Spike fell in love with her instantly!