I'm all in favor of coherent point buy system.
I don't know that you need so many levels. If you want people to run commons, then, sure, commons can be worth something specific, but, if it's really just forcing people to run some rares and more common, then make commons/uncommons/rares all worth the same amount and have people mostly use rares in their low point slots.
As for challenge, I recommend running a token number restriction. 15 or less with the usual four TEs at NM, for instance. Now, it will lend itself heavily to using the same tokens over and over again, so it's hardly perfect for changing builds, but it's significantly more appealing when you go back to PTD - weight, simplicity.
Then, there is a CCG that restricts deck construction by rarity. White Belt Deck is two ultrarares, four rares, 10 uncommons, any number of commons. Principle would be sort of like Rainbow but more like Rainbow Pyramid, with like one dark green, one orange, one dark blue, two purple, two blue, four rare, any number of green or whatever seems interesting that is different from Rainbow.