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Assuming it's not over/undercooked, what differenciates a good and a bad mozzarella stick?

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Well the breading/batter is obviously the most noticable difference. Some places use different cheese (O'Charleys [if anyone else is familiar with it], for example, uses pepperjack which is awesome!) and of course the shape and size can affect the product as well.

Also not to be left out is the sauce for dipping. Many an otherwise solid cheesestick is ruined by a terrible sauce for dipping.

As you can see I share Diablo's weakness for fried cheese.