Well the behaviour of nautilus really doesn’t have anything to do with unity. It is a gnome project and I agree that it is getting more weird by each release (e.g new window and new tab appearing on opposite sides of the panel)
The second issue is also kind of annoying but you can partially make it more bearable with gsettings or dconf-editor : org>gnome>nautilus>preferences to turn off show hidden files. This way it won’t show hidden files by default. but still will show them if you have hidden files shown when you close nautilus the last time, it is still annoying but a bit better than default behaviour of showing hidden files all the time-- why are they hidden files if they are shown ALL THE TIME??
I am sure gnome devs consider these new annoyances “features”. So if you are fed up with nautilus you can try nemo
But there maybe some wrinkles. See the discussions in this thread https://community.ubuntu.com/t/new-ubuntu-unity-iso/2146/252