I agree with your critical comments about omitting a lot of the motivations for Charles Wallace - I would have liked more of that. But I think I can forgive that because this is Meg's movie, and to make it the Meg-and-Charles Wallace movie would have required something radically different. The moment when he was seduced (on the beach) could definitely have been clearer, though.

My opinion on what they were trying to do with the "I love you" scene was Meg recognizing that her father has actually fucked up - not that he was taken away but that he made the choice to go, to leave them in favor of Science because he put that first. And since this is one of the things she's been so afraid of all along, she's stepping up to take that role of parent for Charles Wallace and giving him what she has needed. I think that was foreshadowed by Charles Wallace saying "you mean your father," which was pulling from the adoption thing and from the fact that he wasn't even talking yet when Mr. Murray left. So they barely know each other, really. And I think Meg has a moment of realization about that when Mr. Murray is willing to save her first, so she's primed to go into that moment with Charles Wallace with the thought that maybe he doesn't feel that he's part of the family in the same way as she is. Maybe he doesn't feel that he is loved as fully as the rest of them.