User blog comment:Thailog/New trailer for Season 2/@comment-3207687-20120422200008/@comment-1038387-20120422204614

It would just be bad writing, imho. You spend an entire season with Superman as the only Kryptonian and Superboy as his clone, and both have to accept each other, in terms of "family" and (lack of) power... and then you bring a new girl who already has both family ties and all the powers.

When Superboy was introduced in the comics, Superman was still the only Kryptonian in mainstream continuity. The Supergirl at the time was the Linda Danvers/Matrix gestalt; Kara, Zod, the Bottle City of Kandor were written out of continuity with the Crisis on Infinite Earths. Power Girl existed, but her origin was retconned so often even she found it confusing. So at the time, Superboy filled a lacuna.

When all the Silver Age Kryptonians were reintroduced in the 00ties, Superboy was already strong enough as a character to maintain his image. But in Young Justice, the universe is young, and Superboy has only just popped up. It would be too soon to introduce Supergirl, and if they did, it would be a main focus of multiple episodes (if not half the season), not something they can settle in twenty minutes and then go on with their lives.