There is no treble hangover, there is a season that never got going due to multiple injuries and a ridiculous decision not to advocate for himself at the last England camp.
It is true that John is better than Akanji in the 'John Stones role'.
Yet, our tactics have evolved and (for the moment at least) that role doesn't actually exist. The change in tactics might be because Pep felt teams had worked us out, or through necessity because John just hasn't been available to play it to its full effect.
Regardless of the reason we have been playing with traditional CBs, and on form Akanji has been better. To say the two players are not at the same level when 'playing well' is a moot point, to play well, you have to play, and John just hasn't been available enough.