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.
Ensemble Darkhorse: Cain is easily among the most popular characters of the game going by online comments.
Genius Bonus: Gun-savvy people who read the data files can trace the inspirations behind the weapons:
As an example, Faye's R93 sniper rifle looks like a Barret M82, but has the design history of the Blaser R93.
The Akagi 74 is essentially the AK-74 with a longer barrel and carrying handle.
When fully upgraded, Dan's assault rifle is essentially an light machine gun; this makes sense when one realizes that it's based off the HK416, which formed the basis of the USMC's M27 Infantry Automatic Rifle: an extremely accurate LMG in assault rifle body.
Porting Disaster: Averted. The PC port plays well, flows smoothly, graphics look as good as the 360/PS3 (with an Nvidia GTX460), and most importantly, QTE prompts can be set to display as either 360 gamepad or keyboard. HOWEVER, like many bad ports, the game doesn't let you bind most of the keys near the arrow keys, so left-handed players are screwed. Also, switching the key bindings doesn't change the QTE button prompts away from the default.
Strawman Has a Point: It seems unfair to issue termination orders for all Hollow Children, but Yoshiki demonstrates that they can be overidden at any time, and the Chairman of the Joint Chiefs of Staff is a Hollow Child. A Hollow Child is the ultimate Manchurian Agent, able to infiltrate anywhere.
Also, while Amada rightly calls out humanity for attempting to genocide the Hybrids just for being different, his philosophy also includes elements of social Darwinism and racial superiority that sound uncomfortably similar to something that might be espoused by Khan Noonien Singh or the Locust Queen, which would justify humanity in not trusting him. That's probably why, even thought Dan let Faye live and was against the Hybrid genocide, he was still intent on killing Amada himself.
Given that Faye seems to buy into some of Amada's Misanthrope Supreme tendencies to a degree, the U.S. President is somewhat justified in fearing that she'll turn out to be the next Alex Mercer or Khan Singh.