1. Supergirl was in the Kryptonian spaceship that crashed on Earth thousands of years ago in Man of Steel. Presuming she survived the crash (someone did), then...what...was she frozen in ice for thousands of years? No, I'd rather she just be dead.
2. In general, I am always opposed to duplicate characters. Superman is unique because he's the last son of Krypton and the sun gives him powers unlike anyone else...well...except Supergirl, Superboy, a monkey, a dog, etc etc. Batman is unique though...except for Batgirl and Batwoman. Flash has Kid Flash and Impulse (and the Golden Age Flash). Green Lantern is uniquely powered because of a ring that thousands of other people have (so, not unique at all). DC has relied on this nonsense for far too long as a cheap way to build character recognition rather then actually doing something of value with the rest of their roster. If I were in charge of these movies (or heck, DC Comics) I would get rid of every duplicate character they have and force the staff to build up their roster of unique characters.