Hypersmurf said:
In 3.5, yes.
Completely.
Yup.
Go on, now ask about
Awaken
-Hyp.
Uh... no. Not going into Awaken

.
I think the best way to handle this would be that magical beast rule that was said above. I don't recall any broken things with magical beasts.
Thanks for the answers.
Btw, I have already nerfed polymorphs in my game. They all have stat and natural armour limit. Something like (this might not be totally correct):
Alter self, max stat 15, max natural armour 5
Polymorphs max stat 25, max na 10
Polymorph any object (when used as polymorph) max stat 30, max na 15
Shapechange max stat 35, max na 20
Additionally, unless changing forms to something tiny or smaller, if the caster would have higher physical stat (before magic modifications) than the new form, the old physical stat is not changed. This applies only to beneficial polymorphs.
This way I don't need to think of overpowered monsters that could suddenly become lots better than any older form. I mostly give value to polymorphs as a tool to be used in different situations. I don't want the caster to always have better stats than the fighter after 7th level. With my system, it seems to work quite ok, as now the caster must use higher level spells to be tough, instead of always using the 4th level slots.