Recent comments from Cook have been revealing, I think. My guess as to "what really happened" over the winter is now :
1) the England management bet the farm on Cook as captain when Strauss retired. They'd made an uncharacteristically bold move appointing KP and felt it blew up in their faces, and Strauss, who got the job almost by default, went about it in the most unspectacular fashion and was often also criticised by Warne for poor tactics, had lead the team to success, albeit primarily against an Aussie side who were using Mitchell Johnson as an 83mph trundler, if they even picked him.
Cook's whole cricket ethos is conservative : keep your head down and wait for the other guy to make a mistake, and the management thought he could transition smoothly into Strauss' job with a similar approach, which frankly is the way the English establishment thinks of as the "correct" way to play anyway : for them, grinding to the extent that you draw games you should comfortably win is much preferable to having g+ts spilled in the Long Room because someone gets out hitting the ball on the up.
2) Sadly, Cook's captaincy proved inferior to Strauss both on the field and in terms of man management. I would guess everybody's respect for Strauss' tactical ability went up considerably watching Cook trying to do the same thing and messing it up.
3) When stuff starts to go badly wrong and their tactics are questioned, crap leaders tend to double down.
They become more certain that their approach is correct and that the problem is that people aren't following their orders properly, and they become twitchy about protecting their authority. Protecting their authority in fact becomes more important than the question of whether they're leading the team in the right direction, and the team is in deep trouble when things get to this stage.
4) With Cook's captaincy clearly leading towards the most profound thrashing in recent memory in Australia, KP starts pressing for non-stupid tactical options but is rebuffed, and things reach breaking point as Cook insists it's time for more fitness training to help everyone follow his orders more effectively.
KP discusses matters with other players who also feel the team approach is wrong, but they won't openly break ranks against Cook, leaving KP isolated.
5) KPs position becomes untenable as Cook decides being an all time England great and the best batsman on the team is less important than not rocking the boat about his terrible captaincy, and the management feel they can't possibly bet on KPs captaincy for a second time, or on his long term future as a player.
6) Today! England discard the best batsman they've had for a generation in order to build a "new team" around the key concept of respecting the authority of possibly the worst Captain for a generation, who also now can't score any runs.