Gnome3 and Unity have gotten one thing very, very right. They try and utilize the horizontal space for their launchers. When we transitioned to widescreen monitors, it no longer made sense to have all that stuff utilizing the top and bottom of the screens... eating up the smallest screen dimensions with static tool bars.
Auto-Hide isn't really an option for my tastes, at least on my main window control element, as I like to see what is up and running at a glance. I think after much trial and error I've finally got my setup how I like it.
Plank, fully extended on the left side of the screen and fitted with a custom "Show/Unshow Desktop" clicker, handles all my windows management functions. I have a small MATE panel set to auto-hide up top that has my system tray, clock and MATE Menu launcher it it, so Super_L can still get me a quick search box for apps that aren't on Plank.
I don't actually use multiple virtual desktops or Compiz at this point... someone linked me to a tweak to get tear free video under Marco a while back, so I left the sometimes wonky world of Compiz behind, pretty as it is
Anyway... everyone has their own way of doing things, but this one is mine. I think I've found my personal sweet spot.