Aaron Tveit's performance and body language (especially in I'm Alive, in which his choreography borders on pole dancing) is sexually charged, and Gabe & Diana's duet "I Dreamed a Dance" can very easily be interpreted as a duet between lovers rather than mother and son. But it's brilliant because very early on in the show it has been shown that Diana has trouble putting a filter on her sexuality ("I'm going to have sex with your father."), and Gabe is, if not a fragment of her ill mind in denial, then a spirit influenced by her, ("Although you made me, you can't change me/I'm a perfect stranger who knows you too well,"). So it stands to reason that Gabe would be a little, uh, bold!
On the YMMV page, it is said that Natalie being a genius is an Informed Attribute, but it actually isn't. When we first meet her, she's dealing with a ton of homework that isn't done yet. Ask any highschooler in AP courses and you'll understand that they gets lots of homework. Secondly, she plays piano and is on the swim team, two things which cut into her homework time drastically. Finally, she's supposed to be 16 and yet talks about an early acceptance to Yale College. If the show takes place during her second semester, she should be choosing what college to attend, not thinking about early acceptance. So, when all these factors are added up, Natalie becomes a 16 who has skipped a grade, takes several Accelerated courses (at minimum) and has multiple extracurricular activities. No wonder Yale might take her!
Diana's lines introducing the family in "Just Another Day" all rhyme, except for the one about Gabe, cleverly foreshadowing he's not really there.
"Superboy and the Invisible Girl" is Natalie's big song... until Gabe comes in. When he starts singing, Natalie begins singing the harmony to his part. Because even in Natalie's own song, she comes in second to Gabe.