I typically don't mind Polymorph, but like Midnight, everyone needs to have their stuff statted up ahead of time. That usually precipitates some negotiation as to what are reasonable forms. So, yeah, there's that, which isn't all that helpful for a line.
Shapechange can get things really pear-shaped, though, since there's bound to be some idiosyncratic Ex or Su ability that completely throws things.
Personally, I find Polymorph a little bit too easy. I prefer to optimize gishes and other types w/out it nowadays. If I were going to replace it, I'd probably list a few archetypal forms that I think are reasonable for given levels of play, and those would serve as guidelines. Or, I'd go the route of the Bite of X spells, which is essentially what Pathfinder did.
Actually, don't Frank and K suggest, as one alternative, just using all of the stats from the monster. Meaning, that when you cast Shapechange (and possibly Polymorph, etc.), you are, for all intents and purposes, a Planetar or whatever. I kind of like that, especially for Shapechange, whose primary selling point is supposed to its uber flexibility. So, I'd have 2 lines of spells, the gishy buff one that would be along the lines of a Bite of X spell, and the other just a "use the stats from this monster." Both would probably be pegged to CR, which isn't a perfect measure, but probably good enough, and worlds better than hit dice.
EDIT: there is a bit of thread necromancy here. I'm like 50/50 on the OP's rules suggestions. As usual, I think he overstates things, but about half of the things discussed, or some form of them, have also filtered into my D&D campaigns. I do think that there's a very specific style of play assumed, however. This is also true of Frank & K, but I feel they are more up front about it.
