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.
Double Standard: Chikane rapes Himeko to save her from her destiny, and it's a-okay for many fans because "she did it for love". Try thinking of Souma doing exactly the same thing with exactly the same reasoning... Yes, these same fans would've gone apeshit at him.
Ho Yay: Souma has some with Tsubasa, despite them being brothers.
Informed Wrongness: Souma spends a large part of the anime convinced that Chikane is taking advantage of Himeko and trying to convince her to come with him instead. Given Chikane's behavior, some fans might wonder if he's right.
Memetic Mutation: The ending image with Himeko embracing Chikane has been parodied oh so many times with other couples (be het, yaoi and/or yuri) replacing them. It has been said that a yuri ship is not official until someone draws them in a "miko embrace".