Well, you know there is something to be said for templating the undead. It allows for a wider range of challenges, and reduces weird results. Why should a skeletal tyrannosaurus lose its bite attack? The regular tyrannosaurus has teeth. The skeletal tyrannosaurus has the same teeth. A tyrannosaurus has hardly any arms, and has no leg claw attacks, so a slam or claw attack on an undead tyrannosaurus wouldn't make any sense. It should bite, and do damage equivalent to a tyrannosaurus, with adjustments for becoming skeletal.
So what we need is some other mechanic to balance the various skeletons and zombies. We have two immediately apparent mechanics: hit dice and CR. While the skeleton by size mechanic was simple, it oversimplified. A standardized set of undead templates gives the opportunity for more interesting undead.
Now I think I'm going to have to write up the Summon Undead set of spells for my own use. I'll have to figure out the specifics, and perhaps allow for some of the weirder templates, like Vampire, at higher levels...