That could, however, be easily hand-waved as something to do with the clone. The Nidoqueen was cloned and thus the clone possessed only the genetic material of the Nidoqueen. It's unknown if the clones can even evolve, so it's possible that they only possess the genetic blueprints of the evolution they were cloned from. Thus, if the clone were to breed, its offspring would carry the genetic material of its clone parent and thus resemble it.
Which brings us to another problem... Clone fertility. Clones tend to be sterile, due to problems with gene expression. It would make perfect sense for Mewtwo to be sterile. However, to breed him would require reproductive cloning, which his DNA would be placed within the nucleus of an egg, and then that egg fertilized and grown to term. If additional donors are present, and the embryo grown to term within another animal, then the usual problems inherent with cloning would be less prominent. Otherwise, cloning a clone would produce a very flawed specimen that would likely die shortly after birth, if it even survives to term.
The cloned Nidoqueen's offspring would likely have better genetic stock, as it bred with the Rhyhorn. If that offspring breeds with wild specimens, then its gene pool would be diversified and you could end up with a viable race of fertile Nidoqueens.
This is all assuming that the clones Mewtwo made don't have the usual problems that tend to plague clones. Fertility is a very good sign.