I think, more so than the clones themselves, the children of the clones are the key. I think the audience is being intentionally led to believe that the clones are the "Leda" here, when in reality, I think the clones might represent Zeus, mating with regular humans to produce demi-god offspring.
It makes sense, considering that the Neolutionists are all about advancing humanity biologically, so merely cloning humans would probably be a boring endeavor for them. But biologically altering those clones so that their offspring are born with mutant enhancements? That sounds like something they'd do.
Explains why it's such a big deal that the clones can't reproduce, why it's such a big deal that Sarah can, why people seem more interested in Kira than Sarah despite her best efforts, and explains why Kira has Wolverine's healing factor.
The only thing that throws a wrench in this is Helena, since she seems to also have healing factor, and so far she's the only clone that's demonstrated any advanced human abilities.