The Droid 2 and Droid Pro will both run on stock. The Xtreme will run on "Ninja Blur". Even still, my upgrade is in January and I may wait longer for something better to come. If not, the Droid Pro looks like a killer device.
Stock > Sense because everything is compatible with stock and it's much less of a hassle to hack/tweak.
Android is really fragmented because of these other skins. If every Android phone ran stock, it would be a lot better IMO. Look at the iPhone. One device, one skin. Not a bunch of devices like Android. There's a reason why Google passes out N1s and Droids to their testers. And there's a reason why they're the only two phones running 2.2 while everything is left back. I mean look how long it took the Hero to get 2.1 - almost a year. The Incredible isn't scheduled to get 2.2 till later on in the year and there's a reason why most developers keep producing ROMs for the two stock Android phones.
But you don't know what any of the devices will run.
I respect your opinion saying that Stock is superior to Sense UI. However, keep in mind that for the regular consumers, Sense UI remains to be the 'complete' and 'polished' Android experience. I suggest you should go and listen to the Android Central Writer's Roundtable Podcast on the DROID Incredible, and listen to their thoughts about Sense UI. Very true.
I understand your comparison to the iPhone, though you are somewhat wrong. I've used all generations of the iPod touch, and the hardware is all roughly similar. Not so for Android. You say the biggest factor of fragmentation is the skins, but I disagree. I think it is the hardware. The HTC Hero on Sprint can hardly be compared to the DROID Incredible, though it is running Sense UI on top of Android 2.1. The hardware is inferior.
Technology moves, and Android stays with it. Motorola says it wants a 2GHz phone out, but the fact is that batteries suffer under the current 1GHz Snapdragon. So while I'm sure that it is possible to have a 2GHz chip in a phone, how will the battery be?
My point is that Stock has things missing, or has areas that still feel 'rough' and somewhat unfinished. Competing against the iPhone OS (which is truly beautiful in terms of ease-of-use and simplicity), that just doesn't work. HTC has done a marvelous job of fixing those areas, and adding some eye-candy everywhere else.
But congratulations on your soon-to-be DROID Pro/2. I'm sure it will be a great phone.