Finally found an addon that allows char-specific favourites!
Posted: March 19th, 2015, 4:43 pm
Ok, so it's probably been around for a while (as I last looked a few months ago) but I've only just found it and I'm super excited! All my alts can now have their OWN favourite pets wandering around their garrsions (elementals for shammy, fluffy beasts for my hunter etc) and it works for mounts in the stable too. So now my daughter, who plays undead, can stop complaining that she has to have shiny, fluffy, cute mounts in her stable when all she wants is skeletal ones! 
Here's where I found it: http://www.curse.com/addons/wow/character-favorite-mounts
Here's where I found it: http://www.curse.com/addons/wow/character-favorite-mounts