Ok, I have read the comments, and thanks for those. They have given me a good perspective on the topics and I have an idea on how to move forward:
Instead of having split malls like now, I will rather combine them all at spawn. It is better to have a crowded central spawn than splitting up the people over the map. If we ever extend the map again and have a lot of people online permanently we can think about that idea again.
The /home command
I will leave the /home command as it is. If you die, you should not loose your stuff because it takes too long to get it.
This will depend how the portal making works. If making a portal from the nether does NOT make a portal in the normal world, I will make the whole nether public. If it creates a portal in the normal world, I will either make a portal command instead of people building them or split up the world in sections. Then I might also reset the nether regularly such as one a week or so.