Honestly I don't feel it is much "fun" to look through all your colonies to check for obsolete improvements and delete them.

One example, after terraforming, and having no more hot/sterile planets, all AI labor improvements become useless (sidenote: why that effect is given the flavor form of "AI labor" would another topic for debate :P  Since when does AI only work in hot/sterile? :) )

Anyway... maybe the game could make a simple check if the output of an improvement equals zero, and notify somehow?

+1 to this.

ES1 had a system where you could click a button and all systems would automatically pick out and remove system improvements that were now useless. I'd very much appreciate the same tool implemented in ES2. There was also a system for searching moons and reducing negative anomalies. Given that there is never a time you wouldn't want to reduce an anomaly/search a moon, a simple button to do this in all systems, rather than going through each one individually, would be extremely helpful.

While we're at it, can there also please be the 'ctrl+alt' and 'shift+alt' system which built the same improvement, where able, in every system either at the top or bottom of the queue depending on the combination. It's an incredible pain to go through every system just to make a single building, especially in large empires, where I'd rather manage everything at the empire level through the system screen, than at the individual system level.