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.
YMMV: The Five Star Stories
Ensemble Darkhorse: The Cross Mirage, a lowly recon mech that barely gets any fight scenes is quite popular for some reason, even getting a talking gun named after it in Magical Girl Lyrical Nanoha.
Because Jhon pilots it? He himself seems to be a fan favourite.
Freud Was Right: Check out the details on the Knight of Gold's swords.
Jumping the Shark: The Chivalries arc is often reviled due to the introduction of many a Canon Sue, as well as the creation of a Continuity Snarl simply because Nagano wanted MOAR MECHA.
Squick: If genderqueerness really bothers you this is not the manga for you. Also, a lot of things the less scrupulous Headdliners do with their Fatimas are definitely disgusting by anyone's standards. In fact, a lot of things about Fatimas are kind of disturbing, really. And let's not even get into the weirdness behind the circumstances of Doug Kaien's birth...
If you think that Doug's birth is squicky, just look at Max... That is a well and truly Big Screwed-Up Family. Dr. Ballanche didn't even start it.