Maybe some other primate skull?

@Twilatron217  
More like the humans are the Endless from Endless Space

@Dawn Blast  

@DanielTepesKraus  
i think cr liked it,when he did the big bertha review

the skull on caballeron looks more like a monkey skull than a human one and the skulls on appleblooms could easily be caricatures of pony skulls.

They may not be human, could be aliens, or some kind of non-human ape.

@DanielTepesKraus  
You’re not the only one, I enjoy the movie as well…

They don’t look like human skulls, especially the right one.

@Zennistrad  
THEY. COPIED. ME.
 
Lol, seriously though I think I’m the only one on the planet who likes that movie. I mean, really likes it, it’s one of my all-time favorite flicks.

@DanielTepesKraus
 
That sounds suspiciously like the plot of the Super Mario Bros. Movie.

Another explanation: monkeys (or some variation of them) probably exist in Equestria right? monkey skulls are like ours.
 
Doesn’t necessarily have to be human.

@DanielTepesKraus  
Daisyyyyyyyyyy!

@DanielTepesKraus  
Dammit, man, stop making so much sense!

I’m going to be boring and give the real answer: so that the audience instantly recognizes them as skulls.

Sometimes they dig up these fossilized hominid bones. Nopony’s really sure what they looked like alive.

Because ponies worship Khorne and he prefers humans skulls. They make the best fictures and are quite comfortable.
 
BLOOD FOR THE BLOOD GOD! SKULLS FOR THE SKULL THRONE!

Goddamn it, DTK, that works a little too well. Well done, you bastard.

@DanielTepesKraus  

@Background Human  
A long long time ago, the Earth was ruled by humans. They were the top of the food chain, so not a lot of ponies went around hassling them. Actually, nopony went around hassling them because there were no ponies left. Just the first unevolved horses. Basically, life was good. Then something happened. A giant meteorite struck the Earth! Good-bye humans! But what if all the humans weren’t destroyed? What if the impact of that meteorite created a parallel dimension where the humans continued to thrive and evolve into technicolor facsimiles of modern day Equestrians? And hey. What if they found a way back?  

Remember the Hearth’s Warming Eve story, how the ponies came from some other land? Let’s just say that when they first discovered Equestria, it was already inhabited. Was.

Considering the Pony heads act and look like ours its not unreasonable to assume those are pony skeleton heads.

Humans are the precursor race, long having left the planet. The pony world is built on the ruins they left

It’s best not to think about it.