I know it's a pipe dream and I've already requested it, but besides "The Great Plains" the song I want upgraded most is "Seven" by Sunny Day Real Estate. Again, the drums are amazing, but completely borked for pro.
Also, I never got around to buying the amazing-looking "Complexity of Light" by Children of Nova when it first came out, but now that the drums are screwed up in pro, I haven't wanted to. Would love to buy an RB3 version.
How about Band of Skulls' "I Know What I Am"? That one is practically a duet, so would do really well with harmony upgrades. And again, the drums could use pro-ification.