Pep is always tinkering with his squad and I am sure he already has everything figured out in his head. If Messi goes to City there will be adjustments from both parties but I expect them to click and produce results almost immediately. I am thinking Pep would play Messi as a false 9, while at Barca he destroyed Real in one game with Messi playing just that position. City has world class players on the flanks and this kind of tactics would suit them perfectly. If Aguero isn't fit striker position is a bit weak, Jesus never really shined there so this is another point for false 9 theory.
Only problem is Messi defensive running, he has been outputting seriously low numbers in this category, worse and worse every year. That could possibly prove a problem for City.
I agree with you in general. Messi and Pep combo is the key, not so much Man City, though the quality and depth it has is a clear advantage for Pep. Pep knows how to use Messi and he will adjust both Messi and tactics to produce. It will be instant as you said, cause they both know how to do it, plus Man City is already like Barca 2, with more supstance.