It is a skewed system for naming as it is based on the order these earths have appeared in the series - Zoom's earth is Earth-2 purely because we saw it first, therefore Barry's earth is Earth-1. Supergirl's earth should be Earth-3 based on this order of appearance method, and Jay Garrick's Earth-4... in terms of importance I think going forward Jays earth will be of more importance than Zoom's now finished story of Earth-2, but given the weakness of the Zoom story it is a shame that the name is now associated with his story rather than Jay and the Justice Society. It is unneccessarily confusing.
Looking back on the series it does strike me that Earth-2 is the equivalent to Earth-3 in the comics universe, a world of villains, with one lone good hearted scientist standing against them.
E 3 should be world of the JSA, but my guess is that Barry, by saving his mother, created a flashpoint event that will somehow merge them all together, or at least allow for both Jsa and Kara and her gang as being on his earth?