StartTday - very similar situation just happened to me.
I bought a used 2003 Cooper on Monday - CR/B, all 3 packages, 17K miles
First saw the car over the weekend and went for a test drive. We sat down with the dealer and said "we don't negotaiate, what is your absolute bottom price". He quoted the price that was listed on the car, so we got up. He starts trying to negotiate. Sorry buddy, asked for your absolute bottom price, you said that was it.. so we're outta here.
As planned, he called back and we offered $2K less than the listed price. He said that was absurd, they would take a loss on the car, wasn't worth the money, didn't know what we were talking about etc. etc. etc.

.... then he went for it. I don't think we got a phenomenal deal, but I do think it was a good, very fair deal and I'm happy with it. The dealer on the other hand was forced to go nearly $4K below their original listed price.
I agree. The second hand market is really tough for MINIs right now. I was looking at listings where people/dealers were asking the equivalent of MSRP on a 2005 MCS for a USED 2003 Cooper. I ordered and waited for my first MINI and I'll do it again for the next one. Unfortuantely, the Cooper I just bought was a replacement for my first which was totalled, so I didn't have the luxury of speccing a brand new one
Best of luck to everyone trying to find a used MINI. They're out there... its just a matter of finding them!