Deus Ex and Assassin's Creed take place in the same 'verse.It was stated that the Illuminati had the most power in the 20th century, so perhaps the Templars took over at the start of the 21st? Then the thing with Miles happens, weakening them, allowing them to be mostly stopped wiped out. Then MJ 12 rears it's head and takes over.
Alternatively Deus Ex and Metal Gear take place in the same 'verse.The Illuminati are the successors to the Patriots after they became defunct. The Cyborg Ninja program and GECKO program are the predecessors to the augments that Adam uses, which eventually give way to J.C. Denton's nanomachines once the public begins to trust them again, which they certainly wouldn't after the events of Guns Of The Patriots.
JC is a vampire.This is why he can stand behind a MJ12 trooper who is looking in the mirror and still be unnoticed. That would also mean a vampire can see his own reflection, but the others cannot. It would also explain vampires' facility for the use of hair gel.
JC has passive nightvision.One thing that always bothered me about Deus Ex is how enemies can see you more/less in plain sight, and still not seem to notice you. Also, in a oft-quoted line, JC says that "my vision is augmented", yet at that point it's impossible to have any of the vision-related augmentations. The logical solution is that JC has a passive visual augmentation - he sees much more clearly than the NPCs, so an area that appears to moderately dark for him (ie most of the game) is actually much darker through the NPC's eyes.
JC hears the background music.At the first visit to UNATCO Alex mentions the idea to plug JC into an online Jukebox. Probably that's a relief for him, since there seems to be no effective firewall for Infolink, so everybody and his dog try to chat with him, what probably would annoy anybody after some time.
JC was augmented so that chain-eating candy bars would heal his injuries.He has some kind of augmentation that, after allowing the body to take in a set number of calories for the day (calculated considering JC's size and weight and how much he must burn running around killing people), any extraneous calories that JC consumes are used as energy to fuel some rudimentary regeneration and healing capabilities. It still takes some energy to process the food, especially junk like candy, soda, and booze, so the output is not extreme. It would explain, at least, why his body processes alcohol into hit points so quickly with only a few minutes of drunkenness, because there's an artificial structure in place to make that happen with far more efficiency than regular old organs. (Yes, I've been playing video games for years and it still bothers me when I eat ten candy bars and suddenly my leg isn't broken anymore.)
Hostile Waters is set in an alternate version of the Deus Ex universe...Where a revolution or internal coup threw down both the Illuminati and Majestic 12. The Cabal are the last remaining higher ups of both groups - more MJ 12 then Illuminati. The Creation Reactors are a more primitive version of the Univeral Constructer technology.
The sunglasses and trenchcoat aren't just for showThe trenchcoat is a nanomachine woven, shock- and bulletproof, and contains internal electronics. The sunglasses are similarly made of artificial diamondoids and may have embedded functions. Why? Because it's awesome and sounds like cyberpunk, and it gives an awesome in-universe reason to look cyberpunk.
Walton Simons is Adam JensenIn the Illuminati ending, Jensen joins the higher ranks of the organization, having earned their trust by broadcasting their message. Adam then changes his name, to erase all traces of him before his induction. It's natural to believe that he would go even further up the ranks; and helping Bob Page to form Majestic 12 would be a natural step, wanting to have a more hands-on role in regulating human enhancement. We know from Bob Page that nano-augs are backwards compatible with mechanical augs; Simons is all but the only major player in the original game who is never mentioned once; he looks and sounds like an older Jensen - it all fits!
The next Deus Ex game will be about how Majestic 12 overthrew the IlluminatiYou'll play an experimental prototype for Physiopharmaceutical Augmentation, like what the Men in Black have. Hopefully you'll share their cool robot voices.