At both Lionhead and Improbable we use PyMel heavily. Infact it makes up the majority of our pipeline code. Having an object based wrapper to interface with Maya/Nodes makes coding far easier than dealing with names and strings all the while.
Typically we use it 'out-the-box' predominantly and just keep an eye on fixes that are of interest that we cherry pick ( though we honestly didnt have to do that much at all ). If you choose to get a later release or deploy your own custom version its just a case of ensuring your version comes before the default maya one in the sys.path list.
At Lionhead we switched from 2012/2013/2014 with barely any alterations to our actual pymel code (i cant actually recall any).
We tend to fallback to compiled c++ plugins for anything that requires a node that will be used within a rig just to ensure framerates will be as high as possible, and there is the occasional splash of cmds in places ( again usually where you need to iterate through masses of verts etc ).
We're just building a fresh pipeline at Improbable, and I dont hesitate to use PyMel heavily within the Maya codebase. IMO its a python integration done right.