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.
John's particular goofy way of catching a key card in one cutscene.
There's also the matter of the mutated cow near the end of the game.
Never Live It Down: How Commander Clansy sees his demotion from a submarine commander to leader of an underwater base. The trouble is that his "one mistake" was torpedoing a passenger ship full of civilians in contested waters before a war. In context, his "punishment" was incredibly light. Worse, judging by the way he took it, he views himself as the bigger victim than the people he killed.
So Bad, It's Good: The voice acting. Dubois gets a shout out in-particular with his shrill falsetto fusion between Dame Edna and a South African!
Shipping Goggles: If Deep Fear was bigger than Final Fantasy, than perhaps John and Gena would qualify. If she didn't transform into an atomic beauty to defend a monkey that is!
They Just Didn't Care: The translators didn't even bother to check how to spell certain names (such as "Clancy", which is spelled as "Cransy", or "STORAGE" as "STRAGE"), as it's apparent in the credits.
Uncanny Valley: The FMV cutscenes, full stop. The characters' facial features just look...off. This is compounded by their unnatural, jerky movements and gestures.