I liked Ephraim!Lyon and Trabant the best, I would say.
I only like that route's version of Lyon, though, mostly because we don't actually see Lyon on Eirika's route; we see Formortiis. I really liked the Ephraim version of Lyon, though, for actually trying and often succeeding in controlling the demon king. And pretending to be possessed in order to keep Riev in line was a stroke of genius, too. He's an interesting character, and in a rarity for the series, the game is actually rather subtle about it.
Trabant, meanwhile, is very similar to Arvis, and I'd even say that the two are sort of mirrors to each other. Both of them killed Gen 1 main characters through some form of treachery. Both of them became kings. They both take extreme actions to do what they think is best for their countries. They even look rather similar; if it wasn't for their hair colors, you could hardly tell them apart. The main difference, and the reason I like Trabant more; is that Trabant understands the implications of his actions. While Arvis deludes himself into believing that betraying Sigurd and becoming Emperor was the right thing to do, even as his empire crumbles as a direct result, Trabant realizes that he is a terrible person for what he did to Cuan and Ethlin. And when his adopted daughter seemingly dies for it, it inspires him to lead his suicidal charge against Seliph's group. And he knew that it was suicide, too; he didn't even bring the Gungnir with him. Trabant just had a surprising amount of depth for having a much smaller role in the story than Arvis did.