Not sure which of my 12 issues being more tolerant of metafiction fixes.
For starters, it would help you appreciate what the film was trying to do.
As for your points...
#1 The flashbacks are important because Matrix 4 is about The Matrix (ie, the film franchise). This is why I brought up metafiction.
#2 Zion was run by a Council of (Mostly) Elders. This is fairly common in genre fiction. Not sure why Old Niobe running Io is an issue.
#3 Bugs and her crew rescuing Neo was a provocation. There's peace between the humans & machines. Niobe was reacting to Bugs threatening that.
#5 That scene was beautifully shot (the warm colors, the Buddhist lake house). And it starts with Morpheus tossing what looks like a cocktail out a window, which made me laugh.
#6 The French guy was the Merovingian from Matrix 2. He was a metafictional joke about meaningless cameos in sequels/reboots.
#7 Despite leaning heavily into metafiction, Matrix 4 is still a sci-fi movie. The transhuman heist to free Trinity from her pod was a cool bit of sci-fi.
#8 The digital natives incarnating in the physical world as nanomachines clouds was clever - you're right, though, could have used more personality when in cloud-mode.
#10 It changed into a zombie
video game.
#11) Well he is The One (mostly). God Mode cheats are kinda his thing.
#12. You're mad because Trinity got to fly this time? Can't help you with that.
I thought 4 was really interesting. But I admit, it's definitely not for everyone. In part, that's why I like it - expensive blockbusters that still feel like personal films are rare (and rarely bit hits - James Gunn & Taika Watiti movies being some of the exceptions).