Great questions.
I am in the market and was just wondering out loud if I actually ran into any that were not modified or only had partial Phases completed.
I do have the aptitude to diagnose and fix my own vehicle and as much as I hate to bring it to the stealership for service of any kind, if they are paying for the repair under warranty, I can stomach that pain a lot easier.
After the warranty issue, getting the best fuel mileage is #1 on my list and being able to delete the DEF situation would fall into that cost saving category. I know it would have to be modified to delete the DEF. I really don't have any desire to modify the vehicle for performance reasons as I'm generally happy with the performance of these fuel sippers to begin with. ( If I wanted a GTI, I'd get another one! ) And I also know if I modify it to delete the DEF I would be voiding any emissions warranty.
Thanks again for all the input.
Let me see if I can comment on each scenario with my opinions (many others will disagree)
Scenario 1 - New, unregistered 2015 released for sale
This is going to be overpriced by $15k or more based on what we've recently seen pop up. Due to this factor alone, any potential FE savings go out the window. You're still buying a 7 year old car, just one that's been rotting somewhere for 7 years and has no milage on it. It's only good if you really want a TDI, as it's the last of them, and it's the latest gen engine. It's also good if you drive a lot and are willing to battle the dealership\VWoA when\if you need to take advantage of AEM warranty for the next 11y\162k miles.
You can read all about what's covered and other details in the official documentation.
Scenario 2 - Currently owned, infixed vehicle
This seems to be a bit of a stretch of me, as it would mean that a current owner has given up receiving AEM damage payments, and I cannot see any reason to turn down free money to keep a vehicle you wanted to keep longer and sell anyways (since it's not for sale), and you also probably turned down a very lucrative buyback option only to later sell the vehicle at a loss (as the current value of it won't be higher than what VWoA would've been offering on buyback.
Scenario 3 - Phase 1 Fixed
This is probably the most desirable situation, especially if you can find one that's only recently been fixed, so that you have the greatest amount of coverage left from the balance of the 5y\60k miles coverage. In this case, you run that out until you're near the end, at which point you go in for Phase 2 fix and basically reset the 5y\60k miles clock.
Scenario 4 - Phase 2 Fixed
This is the 2nd most desirable situation, and probably the most common and likely of the different options. You obviously want to grab one that's been fixed as recently as possible in order to maximize the amount of coverage left over.
Scenario 5 - AEM extended warranty expired
This is the one you want in terms of value, especially if you want to delete\mod it for power or FE.
Any of the fixes will eat into the original FE.
A virgin, non fixed unicorn will have the best FE without deletes.
Deletes on a vehicle that still had warranty, only make sense if you drive A LOT and do your own wrenching\fixing. It takes a lot of milage to have ROI from a few MPG improvement in FE while incurring fix costs when\if some otherwise AEM warranty covered component craps out.
Deletes on a non warranty vehicle make more sense as they improve FE and reduce problems going forward while at the same time removing some expensive components that will eventually need replacing.
Lastly, if you're really after the best FE, I would suggest that you look at some of the more recent gassers. There are many newer vehicles that can be in the same range as far as FE which will not only be newer and cost the same, but will more than likely result in lower fuel costs during ownership. Depending on your current area market, diesel might currently cost more than gas per gallon. This also becomes a factor.
Hope that helps.