Familiars are generally tiny creatures with limited attacks. Or in the case of many improved familiars, small creatures with limited attacks. Polymorph shapes can be in the simplest case great big tigers with far too many teeth and claws. It's not always useful but sometimes you just want your enemies pounced on and killed while you sit back and cast more spells.
I'm playing a multiclass wizard who does melee sometimes and could sometimes really use a flanking partner (I have 2d6 sneak attack). My owl can't flank because it is Tiny and has zero reach. I can cast Enlarge Person or Alter Self on my pet owl and have it flank. It might even do some damage itself.