The issue is not denying or ignoring Cook's remarkable career. The issue is, should someone with Cook's recent performances, be a constant in English selection?
Since the start of 2017, across 12 tests, he has averaged 45.14, which on the face of it, seems quite good. Very good even but the reality is, he is not as consistent as his average suggests (a problem with the average system, but thats a separate discussion). By removing merely two innings, both of them doubles, his average would be almost halved. Now, I know, getting a double hundred is not child's play, but to do it after a string of innings where said player is not even reaching 30 is a bad look.
So Cook is no longer the consistent rock at the top of the order he used to be just 2 years ago. And his reflexes, timing and patience is getting progressively worse. Not to mention his inability to even last ten overs and at least get to 30 (he was out less than 30 in 14 of the 22 completed innings). For a team looking for consistency in its top 3, this is not good enough.