Aidinthel said:
As long as we're overanalyzing FiM I may as well link this:
http://www.overthinkingit.com/2011/02/24/my-little-pony-political-economy/
I love this type of analysis. That article makes me want to write a fanfic about a Ponyville French Revolution. Applejack decapitates Celestia. And then the cows rise up and form their own nation state.
And while the hypothesis about Alicorns presented by the OP seems plausible, I'm not sure observation bears it out. Luna and Celestia are the only examples of their kind, for one thing, and they are markedly different from the other species. Most notably, they're either immortal or live incredibly long lives. They're bigger and more slender than other ponies as well, not to mention the insane level of magical prowess they posses. They're something else entirely.
I think the most rational thing to conclude, given the universe, is that the reproductive process in Equestria is entirely alien from the processes we observe in real life. After all, several natural processes, most notably weather, that are ostensibly similar to real phenomena are controlled by pony ingenuity and magic. After all, ponies don't apparently have genitalia, though it may be assumed that Faust is just being polite not drawing it. We've already seen how emotional connectivity and social cohesion can be a catalyst for magic well beyond the scope of any individual. Perhaps the power of love in this universe is
directly responsible for reproduction, as opposed to our world, where it is merely related, if that.
Of course, this makes the explanation for the pervasiveness of dual genders throughout Equestrian fauna a little more complicated at best, and might have some homophobic implications at worst.
God this is embarrassingly fun to consider.