-Multiple sidequests involve mental rewriting technology (the cult in the sewers, the two serial killer sidemissions)
-An email reveals that one of the doctors involved in the latter is friends with the doctor who experimented on Jensen between games
-A bunch of sidequests involve character living double lives and betrayal (the undercover TF29 guy Vincent Black, Louis Gallois the merchant, the real serial killer, the two Illuminati moles in TF29 [one of which is only hinted at if you very carefully read emails and think about how certain interactions can affect alert states]) or fake identities (the whole thing about how "k." is whoever is running Samizdat, how you discover that the original Eliza is loose and the one on TV is an older version the Illuminati used to replace her, which is why she talks more robotically and her propaganda is more on the nose than the first game)
-If you find the original Eliza Cassan, she'll note that something about Adam doesn't match her memories of him but she isn't sure what
-Adam's fuzzy memories between games
-Delara, under the guise of a psych eval, asks Adam about his past, which can lead to options where she tells you the "official" story of the events of the first game and Adam can angrily correct her by telling her what really happened. Delara notes at the very end that Adam's memories are "consistent" as if that was the secret purpose of the eval all along and hints that they're using Adam to find the hacker Janus
-The splash screen is two Adam Jensens looking at each other, one of which has the glasses and one of which doesn't
-If you take the "go to the bank" option when pressed to choose between that and the Church of the MachineGod, in the VersaLife vault there is a box in the corner with a piece of wood covered a glass opening. If you use Smart Vision, you can see a head and torso inside. If you move the wood and stare closely, you'll see Adam's face, with his glasses removed, on the other side, seemingly frozen (
link)