Where to begin? Not only do we get characters returning all the way from Batman: TAS season 1 (giving a cool moment to anyone who's been watching the DCAU since then), but this episode really pushes the whole Cadmus storyline forward a great deal.
We see that people DO see the similarities growing between the Justice League and Justice Lords. We see Batman begin to doubt the other founding members. We see the government try to kill Superman, and we get one of the most brutal battles in animation history.
Even though Doomsday's origins are completely changed, it works in the context of the season.
An overall great episode.