If you take the warranty route, you do have to pay a deductible and if the MCU1 goes out (which it will), you will just get another MCU1 (at least based on current practice). If you go the MCU2 route, you get a 4 year warranty on that subsystem and if anything goes wrong would get a new MCU2 for free / will get the advantages of the MCU2 now. Plus if you sell the car, that could be a reason to get a higher asking price if the buyer knows it is the latest unit vs one that could go bad anytime with a high out of pocket cost.
I usually buy extended warranties but given the cost and the deductible, and the fact this is one of the main systems that would fail, I did the upgrade and will bank the added money for future fixes that I can't do myself...