I added this as a suggestion on Connect in the CRM2015 beta feedback (you may not be able to access & vote). MS seem quite happy the changing the colour from gold to green in SP1 UR1 and again to blue in CRM2015 so why not allow a colour to be chosen
for the entire process or individual stage? <end rant>
https://connect.microsoft.com/site687/feedback/details/1026974/add-ability-to-define-colour-of-each-process-flow-stage-or-per-process-flow
As Guido states, it's not possible without unsupported methods.
Rob
MCTS. GAP Consulting Ltd. Microsoft Community Contributor Award 2011 & 2013