I think the biggest issue with the whole Lyse/Yda thing is that it was completely pointless. I mean, why? You'd expect a shocking revelation like that would be game changing but it changed absolutely nothing. They could have had Yda say "I'm leaving the Scions to help the resistance" and the story would still have played out exactly the same way. Why did the writers even bother with the stupid plot twist if it didn't mean anything?