Well, I've considered it, but it turns out to be too big a change, with more ramifications for most DMs than they're willing to handle. But if I were to do it...
Spirit - as a supertype for all creatures of well..spirit, embodying something that would not have physical form otherwise, like a concept. Most Outsiders fall under this. These have the traits of being banishable, generally difficult to kill permanently(an immortality clause would be appropriate) and a guideline defining numerous spell-like abilities.
Elemental - as a supertype for all creatures embodying a real thing or force, rather than the concept of it. Elementals mostly fall under this. Much like Outsiders, except not as banishable, and a greater focus on supernatural and Ex abilities than spell-likes.
Construct - as a supertype of all the soulless devices and animated things. Some plants fall under this. All brawn and as a general rule, no brains. Higher HD, physical output and DR are the name of the game.
Beast - as a supertype for everything with flesh, in general terms.
Subtypes override their supertype
Plant - Animate plants in general. Comes with plant immunities. Plants up their HD by one step and add DR.
Ooze - Anything without a well defined form. Comes with the amorphous traits. No body slots, and proficiencies go down one level but higher HD and
Humanoid - Just a body layout thing. This defines that they have the humanoid body slots. Straight Humanoid hit dice grant more skill points for their HD type.
Undead - Goes on after other subtypes and turns it to well...undead.
Aberrations - Corrupt, twisted or unusual versions of the type.
Dragon - Makes it big, tough and gets the dragon ability suite.
BUT, HD goes under a separate metric(adjusted by subtype).
Bruiser - d10HD, Full BAB, high natural armor, low skills, good Fort and Ref. Proficient with Martial if they can wield weapons, heavy armor if they can wear armor, one natural weapon type inflicts one size higher damage than usual.
Caster - d6HD, Low BAB, low nat AC, medium skills, good Will. Proficient only with Simple weapons and light armor. natural weapons inflicts one size lower damage than usual. Comes with SLAs
Expert - d8HD, medium BAB, moderate nat AC, high skills, 2 good saves, Proficient with simple weapons and several Martial, as well as light and medium armors.
Theres more, but well...its too big a change and a pain in the ass to convert entire monster manuals.