So, I just came back from the cinema. I tried to analyze the story again but I'm still not that good regarding that. So here are my ideas so far, and sorry for the rant!
It's still hard to even figure out who is the MC and who is the IC between Bob and Helen. They have almost the same amount of screen time so one has to wonder who we identify with the most. Helen's screentime could be said to be that of the protagonist, as the goal of the story has something to do with either the Physics of making the supers legal again, or the manipulation of the population's Psychology to make them perceive the supers another way.
However I'd say on a second watch that this movie has a different feel from the first one. Helen being most likely the Protagonist, we can see that the activities she's involved in are less psychology-based than when Bob was having his little rebellion against the system in the first movie, which involved a lot of deceiving, pretending and living up to one's potential - plus the dysfunctional family relationship was a big part of the story, it was actually its core masquerading as a super hero movie. Here it is more a matter of fighting, investigating, signing papers and saving politicians from helicopter crashes. Plus, well, lots of baby-keeping. This movie is more action-driven in nature and, in essence, closer to our idea of a super hero movie.
I also watched it keeping in mind the elements of Protection and Proaction mentionned by @Gregolas and I can see some of them in the movie, but I may be biased. What stuck me was Bob's confession to Violet that despite his past as a hero, he simply didn't know how to react anymore (in my previous replies I mentioned the various things he did wrong, the poor guy tried). There's this whole idea that they shouldn't have acted at all at the beginning and, most prevalent : the idea that heroes exacerbate weakness in the population, who stays passive waiting for rescue - because it's easier to live that way. It is without doubt the main subject of the story and it can be linked to other threads of the narrative with the right elements.
Interestingly enough Protection, Inaction, Proaction and Reaction share a quad under Strategy (Learning). That makes sense since the whole movie is basically that rich guy's strategy to bring the supers back into light with Elastigirl ; and, in the background, you have Bob learning how to deal with Dash's maths, Violet having adolescence and Jack-Jack's powers. (The kids themselves have to do a lot of baby-keeping, flee from Frozone and the others and save their parents ; they have to create some kind of strategy to succeed.) They might look like two different stories but they actually mirror each other... In the context of an OS of Learning. (And a consequence of Conceiving : had Evelyn succeeded, the population would've had the wrong idea of the supers based on the way they were hypnotised, and they would have adopted her own way of thinking regarding them.)
The problem comes from the MC, IC and RS throughline. I may already be off-marks regarding the OS, but the other throughlines leave me completly in the dark because I still can't figure out who is who. Although I'd go with Bob as a MC since Helen's screentime, as I said, appears to be more that of the Protagonist - and considering Bob's jealousy regarding her function, she might be more suited as his IC. Maybe she's not even IC this time, maybe the kids as a whole are. I honestly don't know, perhaps some of you will feel more inspired than I do!