I think Subeta is a perfect example. The pets are definitely one of the least important things, as is the game play. The BIGGEST aspects to the site are the human avatar system and the forums, but people still call Subeta a pet site.
Neopets does allow for some balance though, which is true, as Syntax mentioned, it depends on the user. But for quite a few sites, it seems like incorporating more things and uses for the pets is either not planned or on the back burner. Not necessarily a bad thing though, again, just calling those kinds of games "pet" is silly.