These are all excellent suggestions! One thing for the PC influence side of things would be to perhaps incorporate the rules of Ultimate Factions into play, allowing the PCs to take up individual factions within the realm.
I would also love to see some more information on Skywatch. Such a cool mystery they toss in there that is then never explored. more information on the disappearance of House Rogarvia would be great too. I get that the idea on these two was probably to leave it up to the GM to write up something that goes well with their particular campaign as it plays out, but I could easily see most groups simply forgetting about it.
To play along with the dynamic options you mention, you could even do something along the lines of having a sufficient number of hooks that biting on all of them is almost impossible. Thus, what is really going on at Skywatch? What is the impact if nobody ever goes to investigate? Same with House Rogarvia? How about Hargulka? If the party allies with him, how long will he hold up his end of the bargain?
Other options that would be fun to explore:
1. The Brevic civil war. Options for how to handle it -- especially if the campaign has adopted Venture Capital and the party is now tied to certain houses.
2. What do certain named NPCs do if they manage to survive? A certain quickling for instance is a pretty prime candidate to escape death, but he's likely to harbor a grudge.
3. What are the rest of the River Kingdoms doing? And what happens if the PC's nation goes against the Rules of the River Kingdoms?
4. Optional rules for treaties with other nations, etc.
Weeellllll...
I think incorporating other rules systems into an adventure should be "out of scope" for an adventure path. Kingdom Building gets a pass because it was introduced in the AP, but the Ultimate Campaign (UC) rules are always right there should anyone need them for any adventure. Is it really necessary to repeat them when there's so much new content to add?
Now that they've improved the Kingdom Building rules, I'd rather them not just re-print the original or the UC version of it. Maybe a "Kingdom Building Lite" ruleset for players who would like to be involved in the mechanics of running the kingdom, but don't want to do so at the level that you need a spreadsheet to keep track of everything. (I like pennywit's idea of letting the players focus on one area or aspect of the kingdom as their own demesne.)
Aside from new mechanics, I'd love to see the AP pages be used for all of the story-based content that fans have identified a need for and create over the years. (Most of the items in the lists above this post are great examples of what I'm talking about.) It sounds like they already need to make room for the CRPG content.
And then to repeat what I said in the blog post, they could remove boring/unrelated "filler" encounters to make room for this new content.