I think in the VS. Thread Rules they have to be comparable. The story is, maybe - of course they're vastly different but nonetheless not a lot are. I personally really enjoy the "Grand scheme of it all" stories that they have, the Titans in WoW and the Xel'Naga in Starcraft II, personally since SCII has a campaign and is made in a different format I find its singleplayer is much better, WoW however has much more longevity and can be VERY nice in some questing areas.
Well I like the 1st SC but I have to say WoW, There is more to do in WoW then in SC. Yea you may have online play like WC3 but that gets old. At least wow has updates on the game play so you don't just have to go around leveling or killing things, nor quest all the time.
SC2 is better but sill Its hard to compare a RTS with an MMORPG Its like comparing a sports car with a hot girl I mean do does two things have anything in common .