I was thinking of how to do Familiars and Animal companions and my first instinct was "But wouldn't that interfere with normal summons?" and while there are a few good ways around this already such as making the Animal a party member I tried thinking of something a bit more solid.
Allow the GM/designer to set up sort of summon channels so to speak or "Summon groups", each with their own individually set summon limits AND whether they can be controlled or not.
Right now the Summoner does something very similar.
That way someone can have their Familiar, via a summon. As well as an additional ordinary summon.
If you want to go the extra step you could even allow summons to be weighted within the channel (As in, "This summon counts as two summons")
Allow Origin/Race Specific Stat Set ups.
While this doesn't have too much of a purpose in the standard game, it might have a bit more sway in someone's custom game.