I'm not saying that Koke should replace Alonso flat out, I agree that they are two completely different players. I'm just saying that a reasonable evolution would be to have Koke partner Xavi in midfield: energy and defensive cover + controlled buildup, good complements. International football is much more pragmatic so keeping clean sheets is very important, but there's a point at which it becomes hindrance.
Xavi playing so conservatively these days and Alonso losing mobility even more means that Spain's midfield would have a lethargic tempo and not much creativity.
The formula has to evolve, times are changing. Playing such possession-dominant football worked when there was tempo and attacking livelihood (as seen in the video), not anymore though. Koke is a buildup player and has all the qualities for it (Positional intelligence, passing intelligence, movement, technical ability). He's shown it in various Atletico games but for a more direct translation, in the u21 Euros with Spain alongside Isco and Thiago.
------Casillas
Azpi-Ramos-Pique-Alba
------Busquets
----Xavi----Koke
Pedro--Costa---Iniesta
You don't need to simply aim to hoard possession and slow down play with Alonso and the double pivot if other facets of defensive play work out. Costa and Pedro provide the workrate up top, Koke and Busquets in midfield, and the defense is infinitely improved with Azpi and an enhanced Alba. Sure it doesn't pragmatically suffocate opposition teams as well as the double pivot system does, but it adds to the overall play greatly in attack (which is important, no matter what) and does give a solid defensive system. You've got Xavi pulling the strings, Koke providing engine, Busquets providing backbone, Iniesta's creativity, Costa's strength, and Pedro's effective goalscoring for Spain. Not to mention that the Costa/Koke duo works VERY well together in Atletico and would have good chemistry in the NT as well.
It's probably too risky to experiment with in the WC itself, but as a transition into the next generation it's the most effective use of the squad's talent. We no longer need to disguise defensive problems with the better players we now have, so why not build on that to make a better attacking force too?