I am one of those who tried the upgrade path and felt it was too painful - for my needs certainly. The long thread on GetDPI referenced in the beginning of this topic was started by me.
Just to put things in perspective:
I was a at a workshop at which the Phase salesman happened to be present (it was not a PODAS thing). I had heard so much about the Phase system and wanted to try it. Needless to say, I was impressed (compared to my 1DX) and the deal was clinched when the sales guy told me the Phase policy was particularly attractive to those looking to upgrade as the cost to do so would be at best 20% of the purchase price of the original, i.e. they would buy back the original less 20% and I thought that was great. I won't go into the details of the encouragement from all the other Phase owners present (and there were several) and the subtle push to 'belong to an exclusive club'. I will note for the record that a senior member of this forum did hint to me privately that it was 'perhaps not such a good idea'. Would that I had listened to him....
So I went and bought the IQ180 'value package'. At that time there was very little information available on used values or new values - I only had the dealer's version of the cost - there were no online prices to compare since none of the dealers would list the price (this was September 2013). Others who had bought it before were reluctant to share their cost of purchase simply stating they had received 'huge discounts'. Well, I got 15% off MSRP and then it cost me $42K, local taxes included.
Just over a year later I saw that my use of the system had been minimal (less than 900 actuations), the reasons were many but mainly I couldn't take the kind of images I thought I could but I still believed in the MF system (I had by now bought three more lenses and accessories). I approached my dealer to ask if I could get the IQ250 which had come out a couple of months earlier and was a CMOS sensor although of lower resolution. I thought I could make better use of it and did not want to give up on my desire to continue with MF.
My dealer told me that since it was strictly speaking not an 'upgrade' but a 'downgrade' since it was a lower resolution back (going from the 180 to the 250), I would have to pay $28K for the IQ250 and give up my 180. I asked what would happen if and when the full frame CMOS back came out. He would not commit to anything. I asked about an upgrade of the camera body when that came out (it was rumored to be very soon). Again, same response.
Needless to say I was disappointed and when my DF645+ had a stuck shutter problem a few weeks later which cost me six weeks and $750 to fix, I decided it was time to bail out. I asked my dealer how much would I get for my entire kit (the IQ180 plus the DF645+ plus four lenses, which had cost me just over $50K), he said he could pay me $17K for it all. At this time, I could see that a 'used' IQ180 was priced at $28K on one of the other dealer's website. Since my back still had four years of warranty left I sold my entire kit through another forum privately.
So that's my story. Obviously times change and prices change, when you buy a car it drops 30% when you leave the dealer's lot. The higher the technology, the greater the depreciation. I get all that, my only disappointment with the company is the somewhat less than candid disclosure of the real upgrade policy. I have no criticism of the company's prices, anybody is free to charge whatever they want for a product that they manufacture, as long as they can get a buyer. I do feel that there is more hype than substance here but that's just my opinion.
I am now a very happy owner of the Pentax 645Z and a bunch of lenses, taking the kind of pictures I could never have with the Phase IQ 180, but I won't go into that debate here.
Hope this helps answer the OP's questions somewhat.
Pradeep