To be honest, I know we all like the narrative of something secret going on because it's fun, but the gap isn't
that huge. Ferrari were ahead for a race or two, and now Mercedes are ahead. That can be put down to the cars suiting tracks.
Traditionally, Ferrari always has this late-season slump. That's been a feature since Schumacher retired (the first time, lol). Apart from the 1 Kimi title, they've always lost momentum as the season went on. It cost Alonso titles back in his day, and it costs Vettel them now (not that he hasn't made enough of his own mistakes). The Ferrari performance drop off is just Ferrari doing what they do best - being unable to follow through with plans. And then they try and get too smart and make weird calls - Suzuka qualifying being a good example.
As for Honda, I'm kinda done giving them second chances and thinking "it'll be better next year". Whilst it was clear the McLaren had more problems than just the engine, it's also clear the Honda engine is still the worst of the four. Yeah it's managed top 10s in qualifying now but there's a long way to go from there.
I completely agree with
@CWallace comment regarding cooling. The Renault engine was always more fragile in the tightly packaged Newey designs, and RBR put a lot of pressure on Renault to improve how the engine worked in that packaging, to the point of their relationship breaking down in a very public way. The Honda hasn't really been that reliable in the STR either, so how is it going to be when Newey gets his hands on it? Unless there's a sudden huge leap in performance, cooling and general reliability, it's going to be a tough year. RBR aren't known for being kind to their engine suppliers, so how is Horner going to react when he gets a double retirement through engine failures?