Fair enough, though from the perspective of the people compiling the team I'd argue that they couldn't choose Root (or anyone else who hadn't been captain, which would rule out Herath with the cut-off date they used) and I think Cook's W/L ratio was much better than KW's in the period which I'm pretty sure was the basis they would have been using.
So basically, I'm with you in that I wouldn't want Cook but I can see how they may well have made the decision and I don't think it's the worst ever.
The main problem with the team imo is that, as others have pointed out, it's been published 3 months after the period in question ended. Had it been published in early/mid October, we'd probably all be going yeah, fair enough (captaincy probably still a point of contention, though).
Dunno why Smith didn't make the team, really