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.
Amberley can be seen as enjoying Cain for his abilities and occasional company, but some lines make her look like a Clingy Jealous Girl, notably when she mentions she'd have found out if Cain was really trying to seduce women he met.
The Cain novels are more or less the only Warhammer 40K media that convincingly continue to portray Necrons as horrific monstrosities to be feared. Cain has only pulled off one win out of three encounters with the Necrons (and only by blowing them up from orbit), as opposed to his constant success against just about everything else. They are also the one threat thus far that he has adamantly refused to stand and confront, reputation be damned.
The novels are also some of the few 40K works that manage to juggle presenting all of the main factions as badasses. The one exception is the Eldar, which haven't been featured except for Cain's mentions of his time as a prisoner of the Dark Eldar, which he still has a bit of PTSD over.
The Orks are a more... interesting case. While they are more often than not the "Original Antagonists" that Cain finds (only to later stumble upon the real threat (Necrons or Tyranids), they are considered the comic relief army in 40K, and the 597th are considered experts at fighting Orks, so it gets played with a little.
Iron Woobie: Obviously, issues of self-esteem are the least of humanity's worries in the Warhammer 40K universe, but Cain has more than enough trust issues and paranoia to disturb Harry Dresden, and self esteem so low that on a scale of 1-10 (10 being the highest) his probably has to be measured using negative numbers. He seemingly goes through his entire life, (Close to 200 years due to Juvenat treatments!) convinced that no one could or should care for him personally, unable to connect with people on any meaningful level, unable to believe he's ever a good person or feel good that he did the right thing, and terrified to trust anyone with himself, lest he be shot for cowardice and deceit. He never actually takes Amberly into his confidence, even after a century of romance. That's just outright sad.