Desktop environments seem to be the biggest culprits. I have GNOME3 and want to remove its default Epiphany browser because I prefer Chromium. This, however, requires uninstalling GNOME3 itself. Same thing with GDM even though I use LightDM.
It's a simplicity thing. If you want to break dependency chains, use custom packages. It COULD be that when that package is installed, things just work, but there's some weird dependency issue that happens when it's not. Ubuntu has come a LONG(and I mean astronomically long) way in the last couple of years in sorting out dependency chain issues. They still rock socks compared to rpm based distros.