if you don't feel you'll use the middle pup then that may be the only good reason. i'd get the 3 pup version just for tha added tonal versatility. granted i rarely use the middle pup on my strats but they are there if needed.
Maybe it's a matter of getting used to, but when I had a chance to play a HSH guitar, the middle pickup was annoying as hell.

It's good to have options, I'm pretty sure that if someone doesn't care about the middle pickup, it's much better to just get the two-pickup version.
Quote by T00DEEPBLUE
There's no point in trying to convince a moron.