Sorry, I know Eliot and Margo are platonic soulmates and I love them for that but also, is it possible that Margo has or at least had some feelings that might not be... fully requited on Eliot's part because of his preference?
It's just those little things, like the way she looks at him sometimes etc, but also, the thing that made me think of this, of her being in love with her best friend not only platonically, is her response to Fen saying "Sounds as if you should marry him" after Margo lists Eliot's good qualities to her to comfort her when their marriage is arranged in a 1x13 deleted scene.
She says "Oh, honey, no. Not his type."
I mean, she could have said that so she doesn't have to explain the platonic soulmates thing to Fen, but the way she says it, with a sigh and such regret...
I can't help but think she would love to, but it's not possible and she accepts that or at least tries to tell herself she does.