Which starter you get will depend on how you want to approach your return to the game.
Third Edition has some nice cards but several characters and I think even some of the enhancements have no special ability. It's difficult to win without specials these days. But that will make an easier transition since you can focus more on the numbers aspect of play.
10th Anniversary is sort of a greatest hits deck, with about half new cards and half reprints of decent cards from different expansions. The offenses in particular are a pretty good core for building a new deck around them, since one is green and gold Exodus theme, and the other is white and purple New Testament theme. It also has most if not all of the different special abilities represented somewhere in the decks: ignore, immune, negate, discard, shuffle, capture, convert, etc.