Last warning, there be spoilers here.
Okay, so the flick revealed that Hydra has so thoroughly infested SHIELD that a large portion of the espionage directorate are secretly double-agents. This could include anyone in SHIELD's chain of command or even members of Coulson's trusted band of loose cannons.
There's also the question of who the Clairvoyant is. Whoever this mysterious master planner is, it's a SHIELD agent. We know the Clairvoyant isn't one of Coulson's regulars, but it's probably someone he knows.
The candidates are:
Who: The assumed main character of the series and the presumptive reason it exists in the first place.
Why: To screw with viewers, I guess?
Odds: ∞-to-1 ... Not gunna happen.
Who: Technical wunderkind Leopold Fitz and bestfriend (and possible love interest) biological wizkid Jemma Simmons are the goofy heart of Coulson's commandos. Fitz designed the non-lethal ICER guns, the amazing Retrievers and other devices, and Simmons has used her chemical know-how to cure incurable diseases and utilize strange alien growth hormones.
Why: Simmons is so saccharine she's practically high fructose syrup, so maybe it's all a cover? As for Fitz, he's been acting a little off ever since the mid-season finally, even saying he wanted to "embrace the change" (echoing the tagline of Marvel's sleeper-agents-secretly-take-over-the-world storyline). He even blew off Skye, his stated crush.
Odds: 10-to-1 (Fitz), 50-to-1 (Simmons) ... Keep in mind these are my favorite regular characters, so I don't want them to go anywhere!
Who: The team's resident badass and pilot of SHIELD-616, aka the superplane known as the "Bus." Some of her past was revealed, but she still has secrets.
Why: Viewers found out recently that May is secretly sending coded message about Coulson's progress - but to whom?
Odds: 7-to-1 ... She always seems sneaky, but it's likely she's spying for the angels, rather than the demons.
Who: The team's resident James Bond wannabe. He initially wanted nothing to do with the team, but soon became one of the team's staunchest supporters, even taking newbie Skye under wing.
Why: He was originally the team's most straight-laced and by-the-book member, but he also made excuses whenever the team clearly broke the law, and in "The Well" he was (apparently permanently) infected with Asgardian beserker rage and began a secret affair with Melinda May. Plus, he killed the only suspect Coulson had for the Clairvoyant.
Odds: 3-to-1 ... I would not be surprised.
Who: The audience's window character turned into something of a Mary Sue. She keeps breaking the law and betraying her teammates, but they keep forgiving her. She's an expert hacker and (former?) member of cyberterrorist group Rising Tide.
Why: She's already betrayed them more than once.
Odds: 50-to-1 ... Some fans (for lack of a better term) have been calling for her head, but it doesn't seem like the producers want to turn the one person Coulson trusts implicitly into a villain.
Who: Coulson's boss (except when he decides not to listen to her). She's tough as nails and doesn't play nice with others.
Why: In the series, she has already sent a few of Coulson's agents into suicide missions and last episode she ordered Coulson's team taken down. In the comics, she was Norman Osborn's righthand woman, immediately making her suspect, but she eventually redeemed herself, working with the Avengers. On the other hand, if the Clairvoyant is a high-ranking SHIELD agent, she may be the best bet.
Odds: 6-to-1 ... She seems so obviously bad that it has to be a red herring.
Who: The paper-pusher from Marvel One-Shot "Item 47" and a moderate thorn in the side of Coulson's team, but he seems to mean well and has humored Coulson's techniques ever since he learned Coulson was alive. He nearly died fighting Deathlok, but thanks to his quick thinking, the agents were able to track the cyborg down.
Why: The Clairvoyant is a high ranking agent who didn't know Coulson was alive before this series started - that fits Blake. Also, he met Deathlok right after the assassin was told to "meet" the Clairvoyant. Sure, Deathlok beat him to within an inch of his life, but that's more life than most of Deathlok's targets so far. Also, that was pretty dang convenient of him to put a tracker on Deathlok that 'Lok didn't notice, and that helped lead the agents to the apparent "Clairvoyant."
Odds: 2-to-1 ... So close to even money, and yet, I could be wrong. One time I thought I was wrong about something, but it turns out that was a mistake.
Who: An old buddy of Coulson's and Ward's former superior officer. He and his partner Trip have been helping Coulson's team lately, even when it means breaking into above-top-secret facilities to learn Nick Fury's secrets. In the comics, Garrett is a gruff agent, known for following his heart over his head sometimes, but generally, he's a good guy.
Why: Everything he's said and done so far has been pretty smarmy. He's flat out threatened to torture and kill prisoners (admittedly, so did Coulson, but his excuse was that he was really sad at the time) and he's helped cover-up suspicious missions. Plus, ABC only contracted Bill Paxton for a handful of episodes.
Odds: 3-to-1 ... It seems likely this guy is the face of Hydra, but is he evil, or just a jerk?
Who: Garrett's righthand man. He's a specialist agent with medical training and a soft spot for Simmons.
Why: If Garrett's dirty, there's a good chance this guy is too. On the other hand, if Garrett's clean, wouldn't it be ironic if his nice-guy partner was Hydra?
Odds: 5-to-1 ... This guy has great screen presence, so if they don't make him evil, he'd make a good addition to the cast.
Who: The mysterious doctor who has known Coulson was alive since the first episode, even if he didn't know everything until sending Coulson after Fury's secrets. He went off-grid recently, so it's anybody's guess where he is.
Why: Before he disappeared, he has repeatedly expressed frustration with SHIELD's methods, and although he was involved with reprogramming Coulson's mind, he wasn't aware of how exactly Coulson was brought back to life - something the Clairvoyant was very interested in knowing.
Odds: 8-to-1 ... While he's opposed to SHIELD, it was mainly because he thought they were too ruthless - not exactly Hydra material, unless it's all a ruse.
Who: In the comics, he's the most whitebread of all SHIELD agents. In Captain America: The Winter Soldier, well...
Why: Yeah, that's what fans wanna know: Why Sitwell, why'dja do it?
Odds: 1-to-1 ... Man, if he is evil, I hope he gets thrown under a bus.
(Special bonus suspect, thanks to Reavyn for pointing it out this omission!)
Who: Not technically someone Coulson knows, but as audiences learned recently, he was technically recruited into SHIELD and he had access to a ton of information (except what Fury kept off the books).
Why: Because he's evil, eeeviiiiiiil!
Odds: 10-to-1 (that he's the Clairvoyant), 1-to-1 (that he's eeeviiiiil!) ... This guy has everything needed to be the Clairvoyant, and there's no reason they couldn't bring him into the show - I just don't see it happening.