While the Thompson drives are poor, there's a good chance it will last. I have a Thompson in my v1.0 Xbox and it still works, although it will get slightly jammed on occasion and I have to give the top of the box a light tap. Then again, I got this box last year so it's possible it was replaced before that.
The Dakota is the same as Duke, but has a green jewel with the Xbox logo, and some other slight differences. I think it was a prototype.
Same as the Duke. The center jewel is a nice metallic green design. And the controller casing itself is slightly lighter in color than the standard black Duke...though you'd have to have the two controllers next to each other to see the difference. Whether or not they're prototypes I don't know for sure...(the premiere issue of OXM magazine showed a pic of of Itagaki playing DOA3 on a dev unit using the Dakota controllers + I've heard some people swear that they got these controllers with their launch day Xbox consoles...mine came with a standard Duke so who knows).
Small update on these NOS Xbox systems at Target stores...they got an official price tag up now (listing them as "Xbox Holiday Bundle") for $99. All four are still sitting on the shelves. If/when the price drops I forsee myself purchasing one for sure.