"I think what many people, especially those just coming into the breed, don't realize is that 1) Ameraucanas are still a relatively new breed and 2) the different color varieties are not the same, except for color.
In other words, in the Ameraucanas, because they are still a relatively new gene pool, and different breeds of birds were used to develop the different varieties - those varieties do not carry the same genetics except for color.
So, when you cross varieties (blue, black, and splash being one exception and wheaten, blue wheaten, and splash wheaten being the other), you are really mixing up the genetic makeup of different breeds of birds - hence, the result is an EE.
To give an example, let's say that Brahmas were used in the original creation of wheatens - so they have some of the genetic makeup of a Brahma (including the recessive trait for feathered legs). Let's say that Orpingtons were used in the original creation of the Black Ameraucanas - so they are carrying bits of the genetic code for Orpingtons. Now you cross wheatens with blacks and you have a mutt that has some Orpington genes, some Brahma genes, and some of the traits we've come to recognize as Ameraucana.
Since some of those genes from the two other breeds are recessive, they don't show up in your chicks, but they do get passed down the line until someone breeding pure black Ameraucanas, or pure wheaten Ameraucanas, looks into their brooder box and sees something that shouldn't be there and they weren't expecting...all because someone thought it would be a good idea, for fun, to breed that black cockerel to a wheaten hen. Perhaps, in years to come, the genetics of the Ameraucana varieties will be more stable, better established, and this won't be as much of an issue - but we aren't there yet. At this point, the only variety that is relatively stable is the Black."- Susan Mouw.