Question said:
Changed Subject Is: Increase to Duration Factor1
1. Add all that apply. Look up the total on the next table.
Same kingdom (animal, vegetable, mineral) +5
Same class (mammals, fungi, metals, etc.) +2
Same size +2
Related (twig is to tree, wolf fur is to wolf, etc.) +2
Same or lower Intelligence +2
Firstly......what is considered "same kingdom" or "same class"? What is considered "related"? Could you temporarily polymorph into something like say, a half-orc, so you could then get a bigger bonus for polymorphing into an orc?
DM fiat.
If you take the examples, and use "modern" definitions, turning a Riding Dog into a Human is Permanent - +5 Kingdom (animal)+2 Class (Mammals), +2 Size (Medium)=+9(Permanent). Oh, and what does (s)he think? Suddenly went from an Int of 2 to an Int of 10. Regular dog for halflings and gnomes, of course.
Things get quirky, though; at what level do you define type? If you target an Undead, what Kingdom is it starting out as? Constructs are pretty obviously mineral in most cases (but opinions will vary, and it's not spelled out). Outsiders?
Related appears to be based on "was once a part of a" from the specific examples; but it's vague enough that wolf fur might get you the related bonus for a Werewolf, or a dire wolf, or a wolf-clan member, or whatever else the DM decides.
As for stacking... DM call. Polymorph changes your type; for spells such as Shillelagh, it's been ruled that it's the status of the target at casting time that determines the effects of the spell, not the status of the target at the current time. But then again, there's also that note on stacking spell effects that "usually" the same spell doesn't stack with itself. You can go around in circles on that kind of thing for a while.
But if stacking is allowed.....
You have an Int-6 barbarian friend? That's sad. Let's upgrade him.
We start with turning him into an Ogre. We have Kingdom(Animal), Class(Mammal) and Same or Lower Int(Both 6). That's Permanent.
Then we turn him from an Ogre to an Ogre Mage. You have Kingdom(Animal), Class (mammal), and Size(Large); that's +9, so Permanent.
Now he has an Int of 14. Let's change him again. I like Dragons, don't you? So we turn him into a Young Adult Blue. Same Kingdom (Animal), same Size (Large), same or lower Int (14).
Oh, wait - but I don't like blue dragons. Let's make him a different dragon. Ah, a Juvinile Gold dragon. Same Kingdom (Animal) same class (Dragon), same Size (Large). That's Permanent. And now he has an Int of 18. Nice boost, no?
Mind you, to do all that, he has to be 17th level, but Polymorph Any Object is an 8th level spell, so that's okay.
Likewise, we could, in theory, have just gone Barbarian -> Blue Dragon -> Gold Dragon, as we technically aren't worried about the second stage timing out due to the ruling needed to keep a staff affected by Shillelagh from exploding.
But umm.... no. Don't permit stacking. Just don't.