I always felt the WoR was really more about the characters themselves, being developed. Setzer, Gau, and Strago become more than just filler in your party. The story during the WoR was basically to find your allies and get your revenge on Kefka. I think trying to add another resistance or Kefka needing more minions would have just convulated the plot at a time where doing so would be pointless. It would have felt "tacked on" so I prefer the way it was handled but we all have our opinions on it.

As for your thoughts on FFII, I completely agree. I'm in the camp of "Leon choosing the empires side on his own" So it never really made since to me. I usually just use the excuse of "it was early in the genres life so we can accept it" but honestly. It was poorly written.