In that future, there were 3 factions fighting: the Bastion, the Pantheon, and the Overseer. The Bastion was the human side - they had the Star robots. Since the Star army went into production, it's likely that at least some part of No Return was implemented too. The damage to elite populations would probably slow the spread of the disease, since there'd be fewer infected people to spread it. Also, the division into armed camps would probably minimize contact between elites and baselines, further reducing the infection rate. So that's why there's still humans.
Cassandra wasn't really created to produce 1 elite - she was mass produced. Since the elite population presumeably suffered from No Return and constant fighting, they needed reinforcements. Some elites would also be removed from the breeding population by virtue of their powers - I don't think Ruby would be able to reproduce for example. Additionally, successive generations of pure elites might not work out so well eventually - they might get freakier and less human each generation. Also, engineering an elite from the ground up let's you pick out their powers. If you want front line soldiers and commandos, you might not want to trust dumb luck to provide your troops.
Actually, 17% doesn't seem to bad considering they have to extrapolate unregistered elites from registered ones. Normally, a poll might take a few percent error from sampling and such. However, the UN has lots less to work with - it'd be kind of like figuring out how many people are going to vote for one canidate based only on how many people are voting for another.
Legacy might also progress in stages somewhat. In some cases, it might only partially rewrite the person's DNA. They don't get any powers, but the alterations might affect their children or something. Some people get hit with the virus and get powers soon, while others fight it off completely. THink of it this way: the people most susceptible, the ones who would normally die or require lots of emergency medical attention, are the ones who get powers quickly - like the Miracle Man guy in 2004. Some people can fight off the disease and get nothing.
Also, adults seem to get powers as well. IIRC, the first elite was 34 or something. The elites getting their powers around puberty are probably coming from children of infected parents or something.