OK was tongue in cheek but there is too much emphasis on software controlling everything in the train (oh actually everything) and as a result they've massively complicated the testing and commissioning process. Also the oversight of Bombardier has been abysmal with the level of issues being quoted above suggests a lousy management of the software build. However, these are allowed out on the mainline so traction, braking and safety systems clearly work at a satisfactory level so what are the issues.
The main issue seems to be Bombardier (Alstom) rather than the use of software as a concept! Other manufacturers (even the much maligned CAF) don't seem to be suffering the same way Derby is.
I'm also curious to see what the issues actually are. Like you say, based on the fact that units are out and about, they clearly work at a basic level, I cannot help but wonder how many of the issues actually boil down to "train built exactly to poorly specified spec". There'll inevitably be quite a few "snags" where the product doesn't meet expectations or spec, but things like the cabs being unacceptable must have fingers pointed at whoever specified the trains (presumably, First Group) - I'd be frankly amazed if that's something that Bombardier were given complete free reign over.