First of all, I understand the impetus behind the new way of doing polymorph, but I'm not sure you got it right. Shapechanging is an old fantasy trope, so it's gotta stay in some way or another. The fix you are giving only works if you make the forms in the spells worth taking. These aren't. The elemental spells, even the 7th level variant, only provides resistance to the element 20. Um, no. Presumably fire shield is still in right, the significantly lower level spell that damages anyone who hits you and gives better protection than this? Elementals are not that strong. Just give people full transformation for elementals and animals.
The other is a fix for Find the Path. Just make the focus something intimately related to the thing you want to find (or intimate knowledge of the thing). Lost city? So adventure to the sacred valley to get the one known cobblestone kept since time immemorial by the monks of whickywhack. But wait, you have to legend lore before you can even know that. Not broken. Or simply use the intimate knowledge to find the way home if you're dropped in the middle of the woods. It's home, not broken. You don't even need to raise the level.
The Wish ability score nerf was unnecessary. By the time people get wish, an ability score bump is not really a big deal. Indeed, to make saves that high level monsters will fail even some of the time, it's almost necessary for spellcasters, as for fighters to overcome DR. In terms of verisimilitude, is it so odd for beings of legendary stature to have legendary abilities?
Finally, I still think that ability damage is better than GP costs for spells. This is a verisimilitude thing. The fabric of the universe is not some accountant making sure spellcasters pay the price.
Generally speaking, as you balance things, remember that many (though not all of course) of the people considering going with Pathfinder instead of 4E are doing so because they feel that the gamist bent of WoTC has gone too far. For me, and my group, and I'm sure some others, balance is important, but less so than a world that makes sense internally.
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