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.
Fridge Logic: Aside from aesthetic reasons, Quake II takes place only shortly prior to Quake IV; however, practically everything has undergone a redesign (returning enemy types look different, architectural styles are dissimilar, etc). However, bear in mind that, in the chance of a Quake II remake with the IdTech4 engine, the game would look pretty much similar to Quake IV. Plus, Quake II was done by Id, while Quake IV was made by Raven.
The "Stroggification" scene. Kane's only reaction to the whole thing is remaining completely silent and only momentarily emitting the same grunting sound, that sounds more like someone getting beat with a stick than someone being brutally mutilated. It might push it into Nightmare Retardant territory.
The Strogg also like using dismembered human corpses (or dismembered living people) as decorations, as areas in this game and it's canonical predeccesor shows. It gets worse: they use them as batteries.