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.
Lilith Sahl in the light novels may be even more sadistic than Dietrich. She gave Abel a chance to save himself because she believed in him blindly... at a time when he was a murderous sociopath who killed millions.
Abel, and certainly megalomaniac Seth may be interpreted as other than 100% benevolent, especially considering their bloody past.
Ho Yay: Tons of it. Abel seems to have a thing for Tres, especially in the manga. Also Radu and Ion. And Radu and Dietrich (Radu couldn't shut up about how beautiful Dietrich was while he was being tortured). And Esther Blanchett and Shahrazad al-Rahman's very special friendship in both the novels and the manga adaptation. And Jane and Mary in the novels. And Jane with Esther and Mary with Paula in the novels.
Lampshaded in the manga, when Esther asks Abel if she's "in the way" while she's travelling with him and Tres to Rome, and Abel's reaction is "Tres and I aren't like that! This isn't a yaoi book!"
It is implied that Esther has feelings for Abel, though the latter sort of treats like a younger sister.
The manga and the novels hint that Catarina also has feelings for Abel. It's most evident in when she's in bed due to her disease, she started crying that she won't be able to live longer so she can be with Abel and is jealous with Esther's relationship with him.
Tear Jerker: Lots and lots of them: Gyula's death in Esther's arms, Ion's last farewell to Radu, Shahrazad's death in Esther's arms, Alessandro's death in Esther's arms, Esther at Abel's tomb...)