Your view is interesting. I enjoyed a lot of get to the goal levels in Octo Expansion, actually, including the (NON-TIMED) 8-Ball ones. Everyone hates on 8-Ball levels, but that one 8-Ball station with the rolling carpet things and stuff was my favorite station of all. One the other hand, I strongly disliked popping balloons, matching pictures, beating enemies within a time limit, and all that stuff. On the other hand, the option to choose a weapon among the given is awesome. In terms of final battles, the idea was so much cooler in the Expansion, actually, but I love the cinematic cutscenes in between each phase in Octo Canyon. I like the radio cutscenes slightly more than the chat logs, but I wouldn't mind if one stays and one leaves, for either. Many people would literally stop playing the series if Octavio's the final boss again, but I like him as a villain. I think it would be best if it tricks you into thinking he's the final boss, but then there's another. But you can't not have him come back; it's almost as though Marie enjoys him escaping. She's keeping him in a sphere of shattered glass held together by a Band-Aid. Another thing though is that I love games where you don't have to be good to enjoy them (one of the reason optional bosses are so great).
I like your idea of side quests, but I think it would still be cool to have more than one story mode, just to get different sides of the story. Maybe 3 this time? Splatoon has one, Splatoon 2 has two, and Splatoon 3 will likely have 3.