Thankfully one of the boss fights is gonna be optional in 0.8.1 (and hopefully later all of them. Looking at you, random spawn boss you have to fight if it spawns) and will effectively just function as another temporary threat if you don't go about fighting it.
The "mysteriousness factor" thing you mentioned is kind of hard to say for our "invisible neighbors" as they have always existed, even since 0.1.0. There has always been something in the vast sky, now it is asking what else is out there in that vast sky that we do not already know of. Though, I don't personally have issues with it but I can say the mysteriousness feels like it is dying out in a way when it comes to the later story events, depending on how you look at it. There are now aliens actively hunting you down and are not even trying to make it not obvious they are.
I also like the cleaning as it is something else to do early on, I only really have an issue with the window cleaning as unlike in old versions, the dirt comes back and is currently WAY overtuned when it comes to it getting dirty again.