I'm not a modder but I can guess you can take a raw file of the mob, edit its looks so it appears different, and whilst still keeping the original, give it a chance to spawn like regular mobs. Maybe you can set it so they both act exactly the same, but unarmored has a X % chance of spawning and the armoured one less.
That's the complicated way of doing it, and it keeps it from working in SMP. I just want an extra skin layer for skeletons and zombies, and zombie pigmen.
Mob Armors (aesthetic, 2nd skin layer)?