I think its important not to throw the baby out with the bathwater at this stage.
If you set aside the period between lunch and tea yesterday, when Cook handed the game on a silver platter to a team that had otherwise been second best throughout much of the series, England's tally would have read something along the lines of "well, we found a decent opener, a guy who could bat at three though would be better at five and a guy who might give our attack some muscle, and got Joe Root and James Anderson back to boot" which, along with some promise from Jordan and Ali, should tick plenty of boxes.
Obviously, there are concerns - Cook's form, his captaincy and the lack of a spinner being the three big ones.
Lets start with the one that most desperately needs fixing - Cook as skipper. I've said it before and I'll say it again, his performances have been so bad that it would make statistical sense to get a good club skipper to play as a specialist captain! All jesting aside, he's clearly overreached by the role and needs to be stood down now before his long term future as a player is affected (bear in mind that, playing as a ranksman for Essex, he was scoring in bucketloads at the start of the season). A replacement is difficult - if it were from within the current side, I'd be tempted to offer it to Anderson. From without, since a return for KP is not really on the cards, its rather harder.
That done, question two is, does Cook need to be rested? I'm 50/50 on this - long term, you'd hope he'll recover form and remain first choice, so I'd like them to stick by him. Though it is tempting to see how Compton, Carberry or Lyth might do for a few tests.
The spin option is tricky. I'm assuming that Stokes will return for the India series - he has to really - and that he will either do so as a like for like for Jordan at eight (Plunkett being the better choice in a five man attack, harsh as that is on Jordan who is a decent cricketer) or, more likely, for Ali at six with Jordan replaced by a frontline spinner. Who? Assuming Rashid really is persona non grata, and that Monty's escapades have made him an unlikely bet, I'd like to see them go with Adam Riley. Kid looks a decent bowler, has time on his side and with some words of wisdom from Swann at least might make the grade...