The way I think might be the best way to handle Animal Companions is to take a page out of the Paladin and Wizard's book and base it off of a spell; only instead of summoning a mount or familiar, you make a bond with a non-hostile beast. If the pet dies, you could re-cast it again to either get a new one or raise the old one (instead of resummoning as a paladin or wizard). It could have similar limitations to a familiar (can't attack, etc), and the Beastmaster archetype could enhance it (higher/progressive CR cap, bonus HP, attack ability, ability to use on magical beasts, etc). That way you could either not have a pet, have a small pet to aid in scouting and for RP purposes, or have a powerful animal companion that boosts your offensive capability.
Now I know that as it currently stands that would put a serious dent on the Ranger's resources as spells are known, not prepared, but there might be ways to mitigate that.