"Number of available buildings must be decreased. Now buildings are too many. Some of them do the same thing without having a roleplay feeling and strategy attached to them, they just add pain of micromanagement instead."
I really like the new building system, but agree that pioneers must have theyre faces mashed with a hammer or something, its abit tiresome to spam all these pioneers and outposts during startup just because it seems better than any other item I can put in my queue.
"Outposts autoupgrade automatically after 20 and 50 turns provided that corresponding tech is researched: Outpost -> Fortress -> Citadel, making each next with higher ZoC and bonuses inside it's ZoC. lvl 3 outpost should become strong defending strategical objects not easy to take over."
I am not a fan of the "Auto-upgrade" feature of outposts, Id much rather like if the ability to upgrade them was placed in an easier accessible location, like in the city that owns the outpost.
"Making resource improvements doesn't pile up a queue in a closest city, however it costs 20 guildar and takes 5-7 seasons. Similar to beta 3. Each additional upgrade cost guildar and takes time."
Really like how the cities have to build everything
Well in general, I only think your number 1 proposal is good, and nr 3 and 4 is worth thinking about. Rest is just because seemingly you miss beta 3, I like most all the upgrades to cities and outposts, of-course missing balance and UI to be in place.
I really hope for the magic to hit the outposts too, they dont really seem very magical, and ill hope they'll add small animation depending on each upgrade chosen for the outpost! 
Edit: Im an idiot, I have to wait for the upgrade to finish before the animation arrives 
Sincerely
~ Kongdej