I wouldn't go into much discussion about his PCS in Saitama, eleven guys skated after him, and only two actually got higher PCS, which is what matters. He would most likely score two or three points better if he skated in the final group.
But if we are thinking about doing different things this year, that would be sticking to his two quad toes layout. He only didn't do the quad sal earlier this season because he wasn't in his best form--which he wasn't all season, but, oh well. Building on clean-ish skates with less quads is something I would advise at this point, because Misha is not a teenager anymore, he can learn how to compete with his three quads, but I don't think it's something achievable for an entire season, or for next season. This entire year was a bit of a bust because he was never in shape for his layouts, and with his health in order we could have a better idea of what he can do, but at this point it's anyone's guess.
Now, on to a possible layout, leaving one of his jumping passes for a toss between flip and loop, awaiting what he would like to work on during the season, he could go for something like this:
4T-3T
4T
3A-2T
3L (3F)
--
2A-eu-3S
3A
3Z
Doing a 3S-eu-2S is ridiculous when he could get 2-3 points more with a 2A in place. Also, if this layout turned out to be 'easy' for him, why not take notes from Eteri and push his harder jumps to the second half like the quad toe, or even the quad combo. But first, he needs to be in shape.