Leicaman,
I was very much in your position just a few months ago, but not from a deer, but rather a wearing camshaft . My all black 2005 GLS TDI was in perfect condition with real leather, wood, etc. but I was told by the dealer that the engine stumbling was the result of a wearing camshaft, which would make it the second camshaft replacement at only 148,000 miles. I needed more reliable transportation, but I didn't want the expense of an extra car (if I kept my Passat). What to do? I found a "new" all black 2015 Jetta SEL TDI DSG here in Houston, TX at my local dealer and bought it with a great discount and 0% financing. I put my 2005 Passat TDI up for sale here on TDIClub and that famous auction site, with full disclosure of a wearing camshaft. Someone from Pennsylvania flew to Houston, bought it, and drove it back to PA with no engine issues. Go figure. That was the last I heard. I sold it for $1,500. The moral of the story is that you will find another car you like if you choose new - just start test driving some - gas and diesel. Honestly, I cannot tell my 2015 Jetta is a diesel. It drives and sounds like a gas engine. Alternatively, you can find a 2005 Passat in black somewhere for parts; you just need to look. However, I felt the same as you in that even after the balance shaft upgrade, rebuilt suspension, Panzer Plate, and lots and lots of new other parts, I still had the transmission to think about going bad, and every other thing I see posted here in the Club. I can't tell you how awesome it is to be driving something new with no miles and no worries, backed by a warranty. I treated myself to a satellite radio subscription and love the new tech on the new car (e.g. back up camera). One of your worst case scenarios is that you buy back your Passat, spend time and money repairing it, and then your transmission and whatever else still go bad (and they will eventually). You could easily be looking at $10,000 in repairs in the next 2 years, considering your current damage and the future repairs (tranny, etc.). In my opinion, a new car makes sense when you run the numbers and consider the reliability, technology, warranty, and feeling a new car brings. Having said all of that, I would have kept my 2005 Passat and fixed it if my wife was not as smart and gently convincing as she is.
I still feel torn. Best wishes.