Wow. I never even considered that they would differ on something like that.
That's a substantial hit on the "it just works" front. Some apps will not be able to do anything useful without this. Some people won't understand why.
The reason why is that Qualcomm and most 3G chip manufacturers bundle GPS, as it is required by federal law for 911 service. Just adding a standalone GPS module to the Wifi version would probably cost about as much as adding a 3G chip.
Btw, does anyone else find it striking how much patent licensing adds to the cost of a device? I'm pretty sure Apple is passing the $130 3G upgrade along at almost cost. These 3G chips have been out for years now and probably only cost about $10-20 to manufacture, yet every 3G cellphone manufacturer gets raped by patent licensing costs to the tune of $100+.
It looks like both the wifi and 3g versions have a digital compass, as well.