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I see the problem now... So in my case there are two apps that take long to load so I start doing other stuff and at some point my clicks start to be blocked by the still invisible, under construction app windows... 

Could we perhaps make a blacklist of apps/processes which are not allowed to steal focus? They had focus when I started them and they started loading, but lost it. In that case they would not be allowed to get it back without me explicitly focusing them.

At least that's the idea although the app in question has child processes and I have no idea how those affect things...

It drives me nuts that apps are able to steal focus: if an app is loading in the background then it must never ever just pop into the foreground when it finally managed to set up its window. It would be great if that could be prevented.