These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Genius Bonus: Some of Nemo's lines take on a lot more meaning if you understand what her name means in Latin.
Les Yay: Alice adores Nunnally, and flat out tells her that she loves her in the end. This makes Nunnally change her mind regarding her father and mother's plan. There's also the canon Les Yay that Cornelia felt towards her half-sister Euphie...
Nightmare Fuel: The first time Nemo surfaces through Nunnally's repressed anger is utterly jarring, especially in contrast to how gentle and warm she outwardly seems.
Pandering to the Base: The author admitted in the final volume that some of the major changes to the storyline were influenced by him being a Code Geass fan. These changes including saving Euphemia and Lelouch from dying.