ubuntu-mate-desktop is a meta package. It's like a list of what other packages that it will install, in this case, it's just the packages that come pre-installed.
Removing this will not have any effects, they say it could affect upgrades, but I didn't have this meta package installed while upgrading 15.04 → 15.10. 
If you was to install it later, then VLC would want to install the version that ubuntu-mate-desktop (pre-installed) states.
It's been removed by default in 15.10, replaced by ubuntu-mate-welcome to install a handy choice of apps or install other software managers that are not as resource hungry or slow as Ubuntu Software Centre.