- For starters, the Assassin Contracts you intercept are a lot less... heroic, in Rogue. In Black Flag for instance, you were often tasked with killing slavers, poachers, gang leaders, generally keeping the peace. In Rogue, however, a lot of the Contracts are about the Assassins trying to keep their power; couple of the contracts are about killing people investigating/trying to stop gang activity, and one guy got marked for death because he wasn't trading solely with the Assassins, for instance.
- Not to mention, the Assassins are much more "overt" in Rogue; like you said, they're often shown using chemical weaponry and gang violence in public places, and a number of Contracts explicitly request for the target to be killed in public to spread fear - isn't one of the Creed's main tenants supposed to be "stay discreet"?
- Also related, is that the majority of Assassin-run locations are much more run-down and poor; it's not until Shay comes along and starts renovating these areas do conditions approve.
- The game also points out that the Assassins aren't really the most consistent with some issues; for instance, they're fighting slavery in one country, but actively helping out the slave trade in another. Notably, the Assassins don't even really comment on that, stating that it's more about "fighting the Templars" than anything else. Granted, the Templars aren't exactly innocent in all this, but...
Pretty sure I had some other plot points in mind, but I can't remember currently; I think that crash deleted everything.
Anyways, it's nice to talk to someone willing to actually converse about Rogue; lot of people just seem to be parroting TV Tropes on the game, stating stuff like Shay being "short-sighted and naive" and a "Designated Hero helping out slavers" while ignoring everything the Assassins have done. Seriously, just take a look, if you want:
https://tvtropes.org/pmwiki/pmwiki.php/Fridge/AssassinsCreedRogue,
https://tvtropes.org/pmwiki/pmwiki.php/YMMV/AssassinsCreedRogue.