There is still one problem though. For both of the parents to be earth ponies, that would make earth pony the dominant allele. For them to have a non-earth pony, then they would both have to give their recessive alleles. This would mean that both kids would have the same alleles in order to not be earth ponies, which should make them the same.

The only answer is that unicorn and pegasus alleles are of equal dominance, and one will randomly beat out the other.

unicorn and pegasus genes are both dominant...

How else would alicorns exist if not through Codominance?

this is a problem :|

But if they are both dominant, the parents would not be earth ponies. Maybe all three can be dominant. Any allele can overcome any other, and every once in awhile there is a mutation where unicorn and pegasus alleles are both physically expressed resulting in an alicorn. Or it's magic.

yup... that's magic. Solves all our problems :D

celestia, shes both unicorn, pegasis, and earth pony

Now THAT, my friend, is the most bizarre scientific conundrum since the Missing Link.
There's a 2-million-dollar for whomever can figure out alicorn genetics first. The Institute of Biological Studies in Canterlot would love to hear your theories, so GET TO IT!

allicorn

Doctor Whooves.