The failure seems to have two reasons - overly optimistic promised payments to the treasury, and failure to achieve expected revenue.
The first does seem to be an inherent flaw in the franchising system, and the DfT has to take responsibility here too. If we are to keep private franchises for our InterCity lines - and it's worth pointing out that most similar European countries don't follow this model - then there needs to be something done to avoid this happening.
The second seems to be a more direct failure in the specific case of Stagecoach/Virgin. I think they thought that both business and leisure travel on the route were more robust than it was, and it wouldn't surprise me if market research had lead them to that (incorrect) conclusion. My suspicion is that the removal of East Coast Rewards is in and of itself not as important as some on here have made it out to be, but I am sure that alongside difficulties in providing the first class service, and rises in Advance ticket prices, that it is part of a set of circumstances that have led to the business travel market up the East Coast performing less well than predicted. Alongside this, I think that they've also operated under the assumption that things like Beam and free WiFi will encourage leisure travellers, even where prices have gone up. Again, I can see how focus groups or consultations might have supported this assertion; but either they've raised prices too high, or people's behaviours haven't matched what they said they'd do. Alongside this, circumstantial factors - increased terrorist threat, Corbyn-traingate, misguided branding, wider damage to the Virgin brand - have hit them; none in and of themselves enough to sink a franchise, but enough to do fatal damage to a struggling business perhaps.
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Edit
The irony is that I don't think their (standard class) service has been that bad. As a commuter up the ECML and a traveller of longer distances every couple of months, my perception is that over the last 5 years - ie, both with East Coast and VTEC - we've had a pretty decent increase in the number and speed of services. Certainly, I have now more, faster and (in my experience) less heavily loaded trains when wanting to travel to/from London. And my commute is remarkably punctual, with seating also available on >95% of journeys, and it's almost other TOCs who fall down on that front, not VTEC.