It's ALWAYS better to build a marketplace or a research center or a constructor than to upgrade a building. By the time those buildings might provide bonuses, you're better off building military ships. In other words, upgrading factories and generic buildings (with the exception of the colonial hospital) is a LOSING strategy. You're pretty much always better off building something else.
Not sure I agree with you, tbh. 5% per building leads to considerable increase when applied colony-wide. Given a 10 factory planet, you go from +250% to +300% industry by moving from level 1 to level 2. That's a bonus equivalent to 50% of RAW production, just from going level 1 to level 2.
Remember, this is an economic thing. Given the massive decrease in total available industrial bonuses, 5% per building is now much more valuable than it was - you won't get much over +300% or so on most planets with level 1 buildings, so being able to pick up an extra 50% just from going to level 2 is actually a substantial boost.
* Building Level bonuses severely nerfed (now most offer just 1% increase).
No tall empires anymore? Why?
tbh I was expecting more.
You still get tall empires. Tall vs Wide isn't actually anything to do with adjacency (it's about spending resources building up a planet as opposed to spending them building another planet instead), and tall isn't actually nerfed by this any more than wide is (if anything, wide is hurt more, because it was more dependent on fewer buildings with high adjacancy bonuses).
Building levels were nerfed because they were ridiculous.
Consider: a 7-hex with 1 durantium refinery surrounded by 6 factories. The factories are all level 5, the refinery is level 6. With the per-nerf bonuses, each factory provided 25% output itself, and then a further 25% from the adjacency bonuses. You'd get a total of +330% industry output, and more than half of that was pure adjacency. Later on, you could beef up those bonuses even further; level 15-20 is not hard to achieve on a hub. Buildings were worth less than the clustering effect from the very start of the game.
Now, the same set up will give 150% basic industry and 36% from the adjacency bonuses - still considerably better than the same number of buildings without adjacency, without completely overshadowing the buildings themselves.
Bonus from Colonizer not working. Or at least it's not showing up. 100% manufacturing, 100% social production and yet my new planets produce buildings at the rate of raw production.
Look in the govern screen under the military vs social slider. This is where the totals are shown, rather than on the main planet screen. Any bonus to social or military manufacturing can only be seen here. You should note that social output is always at least 5 for normal planets and at least 10 for colonizer races.