If late in the game and I conquer a planet and a I get a technology
that updates my planet improvements (like factories), I wish I could
either refuse the technology or choose whether to implement it.

I often get stuck with all my planets updating to "better" factories.
If I don't go through and manually delete all or most of them, my economy
goes into the dumper. Let me make the decision whether to update.

This can happen several times a game. I may be deliberately on enhanced
factories and then I get hit with expensive manufacturing centers.

It can take me half an hour to undo the damage of an unwanted technology.
Or I eliminate half of them and even with the most advanced govt I have to
keep building stock exchanges.

I don't think there is an option for this. If not, there should be.