A few more ideas off the top of my head from my latest read-through...
What about sizes smaller than Medium?

Does increasing size give all the stat bonuses and penalties for that change (+STR, +CON, -DEX) included in the package? If not then I think the size increases are over-priced. Natural armor boost for size increase is a "maybe" on that count... maybe the upgrades that would come with the size increase are half-price?

I don't see anything for adding burrowing or flying movement... swapping a ground speed for a swim speed should be free, but adding one should not.