I believe they aren't using the Milestone characters right now due to some licensing contracts with the original creators. I remember hearing at NYCC that DC had some bigs plans for a Milestone push, but these legal issues had to be resolved first.
I believe is was due to the Milestone people thinking they deserved more money for the property, but to be fair I'm not 100% certain I'm remembering that part right. I do konw there are some legal issues, and when they are resolved more Milestone characters will be appearing like we see in Young Justice. Or at least that what was told to everyone.