I am not sure if polymorphing creatures is a viable tactic. First of all
a simple 'dispel magic' reverses it, if this is cast as a 'war'-spell
then you suddenly have a unit of 100 horses crushing to their deaths
(with a little bit of luck above their own units). Since the sudden
appearence of such large pegasus units is rather strange, people are
bound to suspect this. An other problem is that the polymorphed
creatures become the creatures not only in body but also in mind. This
means that they will have to be trained again and everyone knows how
difficult this can be. The riders will also have to be trained. In the
end creating a flying unit through spells might be still very expensive
and the results are unit with a dangerous weak spot. It would be much
simpler to create the mass fly spell and it has got the same risks.
As for skeletons and zombies, you just pointed out one of the most
dangerous aspects of a necromancer. The sole way to destroy an army of a
necromancer is to kill that necromancer or to be equiped with certain
quest spells. The problem is that for the spell a reasonable complete
body is needed and these are not very common. the bodies also can not be
reused for that reason.