The most UNPOPULAR faction in Heroes 5.

Why did the Cyclops forget how to throw stones?

Where does it say that Cyclops should throw stones? And yes, what's wrong with Goblins?

Besides, they have become ugly and grown hooves!

I think they look quite normal. And they inherited hooves from demons (probably). In any case, that's the design of the race; Orcs are mutants, the result of a cross between humans and demonic creatures, hence the hooves. It's a bit strange for a Cyclops, but still, it's logical.

The only flying units the Barbarians ever had were THUNDERBIRDS!

So what?

Who had the crazy idea to replace them with Wyverns, which absolutely don't fit this race?

I think they fit.

Why didn't they remove the standard one for the Dwarves then?

Well, they replaced magic with weakening for the Orcs; it's all fair.