Raiden is constantly referred to as "jack the ripper" his deadname used by his "father" (who abducted raiden and murdered his real parents) during the Liberian civil war.
In game the is referred to this name by a boss
Unusually for the Metal Gear series, the villains are not terribly interested in nuclear weapons, and none are used during the story. There are some more conventional explosions, but none so drastic.
Child abduction and trafficking is a major aspect of the plot. Their brains are being removed to use as cyborg killing machines, and Raiden's own backstory heavily involves his abuse as a child soldier.
Yes, and no. Cops are seen as useless, and the player is forced to murder dozens of them in order to progress. However, there's also a scene where the player is guilttripped into feeling bad for said cops by claiming they have "no choice in the matter". ...When the matter is killing innocents.
Raiden has PTSD and at least three other characters mention their trauma. A power Raiden unlocks midway through the game falls under the "evil alter" stereotype.
The scene referred to is ambiguous and requires context. Raiden was horribly traumatized his entire childhood, and as such it would make sense for him to have an alter. Whether or not it is "bad" representation is up to the viewer.
No, but the final boss is a presidential candidate who says the phrase "make america great again." While the obvious connection was unintentional, it's still very uncomfortable.
Reoccurring easter egg throughout the game of pin-up posters covered by caution tape. The tape can be removed in blade mode and while the women still have (very skimpy) underwear on in the photos, it's pretty suggestive.