Well, I know that in the Starships book for Trek, there will be guidelines on using PC advancements to improve your crew's ship, so IMO, there shouldn't be a problem using some of your own advancements to improve an animal companion (like a horse or a pet). The costs would still be the same (and as a Narrator, I'd treat the skills listed in the creature's stats as racial skills for the purpose of advancement), but tghe PC would be sacrificing his own improvement for that of his steed/pet.
Doug
Former Decipher RPG Net Rep
"Doug, at the keyboard, his fingers bleeding" (with thanks to Moriarti)
In D&D3E, Abyssal is not the language of evil vacuum cleaners.