“Some packages were not marked for update.
The update of these packages need some others to be installed or removed.
Do you want to update those too?”

For users who don’t understand “linux stuff” - what is the best?
So far I always marked everything and no idea if it is bad or good.

I would agree that this message could be improved. I think those are suggested updates, but not needed in terms of dependencies. Those packages to be marked are mostly fundamental stuff like linux kernel, etc.