The Ubuntu Linux distribution is moving to the MIR display server to replace the ageing Xorg display server. This is intended to allow the development of the next-generation Unity desktop. This means that you will be able to use the one Unity desktop on a television; PC monitor and a phone with the one interface. That is quite revolutionary indeed. The Unity interface is quite adaptable to dual monitor situations, this is doable with the Unity-Tweak application for Ubuntu and Linux Mint. I prefer the MATE desktop over Unity though. How will a switch to a new windowing server that takes full advantage of hardware acceleration affect other desktops? I guess that using a different window manager that fully supported the new features would be the way to go. You would still be using the MATE desktop but it would have a different appearance. That would be fine. You could use the kwin window manager with MATE if you wanted to; that would change the appearance of the windows. You can even use metacity with KDE to customise the desktop. That is how flexible the Linux desktop environments are. And moving to a hardware managed display server would have many benefits.
The desktop would perform better and many of the annoyances present in the existing Xorg implementation should be fixed. But we also need good quality open-source drivers for the ATI and Nvidia hardware that allows those cards to perform at their maximum without any problems. There is a list of all cards that are supported by the current open-source driver for ATI hardware on the ubuntu WIKI: https://help.ubuntu.com/community/RadeonDriver. There is an online peition for open-source BSD licensed drivers for the Nvidia hardware. Sign this petition here: http://www.petitiononline.com/nvfoss/petition.html. Hopefully we will see this in the future. For Nvidia hardware on Linux, here is a list of all cards and their current status: http://nouveau.freedesktop.org/wiki/HardwareStatus/. This is not as good as the ATI open-source driver, but this is a step in the right direction. Getting proper open-source drivers would make it a simple matter of enabling support for the card in your kernel and re-compiling it to get your card working. Intel have full Linux support for their chip-sets; but they are only integrated chips.