The '05 Wee will be a great bike. The '08+ beefier alternator is useful if you run electrical accessories a lot, especially heated grips and heated jacket, but it's certainly not critical. And the single-spark heads are theoretically not quite as efficient as the '07+ dual-spark ones, but that's hardly a critical thing either.
My biggest question would be, what's the seller asking for a price? I've noticed that a fair number of sellers have been significantly overpricing their Wee-Stroms lately; I would say an '05, even with such low mileage, should not be more than $3500. If he's asking more, try to talk him down.