Chronicle/WMG

The sequel will include the emergence of Telepathy.
Whenever one of them were in trouble, it triggered a Psychic Nosebleed. This seems like a psychic bond the three of them shared. Perhaps, in time, a telekinetic will start to display more overt mind reading. Since Jean Grey from X-Men, telepathy has been a natural compliment to telekinesis.

The mysterious object was a Kryptonian artifact
A that gives people superpowers?

Matt will be helped through some of his problems....
.... by Dr. Niles Crane, who still lives in Seattle.

The object the boys found isn't the only one of its kind
Other "crash" sites (or whatever that was) are in different places of the world, either more remote and not discovered yet, or discovered by people who've still kept their powers under wraps from society.

Possibly becoming a supervillain by the name of
 * Don't really see that happening, as the matter of superheroes/supervillains was totally and utterly averted in the movie, and I have trouble imagining that they'd reverse that in a sequel.

There are no superhero comic books, films, or cartoons in the film's universe
The kids never compare themselves to, say, Peter Parker or the Fantastic Four, and no one uses the words "superpower" or "superhero". It's next to impossible that the boys, having lived all their lives in America, with normal access to TV, cinema, etc., have no concept of superheroes or have never been exposed to any form of superhero media. Perhaps they simply don't exist on this Earth?

The origin of the boy's powers has to do with Slendy.
As mentioned in the YMMV page, the scene where the get their powers is remeniscent of Marble Hornets. Who's to say Slendy's not creating a new breed of Proxy so as to kick-start his next plan. The object could be an egg that will hatch into a Slender Man.
 * Um, I noticed a particularly strong lack of a tall, sharply dressed fellow throughout the movie, so I'm guessing that's a no. You could say he just wants to hide his hand, but come on! We all know what a drama queen Slendy is.

As an alternative to the above theory, Slendy ressurected and reanimated him, thus creating Totheark.
Think about it. So far, we haven't seen Totheark's face yet, and Slendy could have either wiped parts of his memory so  would forget about his powers or took his powers away somehow. In addition, Totheark and  both seem to be kind of bitter in general, as shown by a line in one of his newer videos: "How much do you hate?.

Also, we have, "Enjoying watching you suffer. Do you know me? I will always know you.". The first sentence alludes to. As for the second and third sentences, there is a possibility that  somehow remembers Matt , leading to   hating Matt. Now in personality, Jay is similar to Matt, except more serious. So Jay reminds Totheark/ of Matt, sparking a desire for Totheark/  to kill Jay himself.

Finally, the mask. There are two conclusions that can be drawn from this: Slendy gave him the mask, or Totheark/ created it to cover   and whatnot. It may also symbolize  taking on a new identity, rejecting his old life in favor of being Slendy's new servant.

Andrew's dad became a shut-in.
With the death of his wife and son, he spends the rest of his life watching TV, ignoring anybody who knocks on his door. He does periodically cry, but only for his wife. He's glad his son dies. He still believe he was selfish. And then he sees him as a freak and no longer his son. He tells himself it's Andrew's fault for everything and not himself.

Richard's hatred of Andrew stems from his viewing Andrew as competition for his wife's affection
Richard does seem to genuinely love his wife, but at the same time, seems to genuinely despise Andrew; and even goes so far as to blame Andrew for his wife's death. Maybe Richard had something of a reverse Oedipus complex going on and resented Andrew so much because he secretly viewed Andrew as competition for his wife's affection. The affection Andrew's mother gave him, Richard viewed as affection he wasn't getting from her: He wanted her all to himself. Richard initially just resented Andrew for it, but over time the resentment evolved into full on hatred; which is why Richard reacts hostilely to practically anything Andrew does. Richard's drinking, lack of a job, and wife's failing health only intensified his hatred towards Andrew, whom he began blaming for EVERYTHING wrong in his life.
 * Another reason is maybe Andrew's birth was an accident. Richard didn't want any kids at all, he's perfectly happy with being just the two of them. But when his wife is suddenly pregnant, he didn't take it too well (but didn't say it out loud). Though he tries to get use to the idea of being a father. Eventually he started venting out all his repressed anger towards Andrew, in addition to other problems.

If there's a sequel, Matt will be on the run from the US government, and possibly other agencies as well.
The Battle of Seattle demonstrated how apocalyptically dangerous a kineticist can be when they lose perspective and moral restraint. The police were literally powerless to stop Andrew even when he was heavily burnt, doped up on painkillers and recently awoken from a coma. Even in that state he still had enough power to toss cars like tennis balls and wreck buildings. It required the intervention of the only other kineticist present to stop him. If we take the theory that the movie consists of the government piecing together confiscated or recovered footage, Matt is to their knowledge now the last living kineticist. As Andrew aptly demonstrated, regular laws and law enforcers simply don't apply to kineticists - they have enough power to, if they wish, make such agencies entirely irrelevant. There is absolutely no compelling reason for a kineticist to follow any law except personal choice. If I were a high-up in the US government - or indeed pretty much any other government - I would be freaking out. Matt's own moral code and mental stability are really the only things standing between him and becoming as bad as - if not worse than - Andrew. He's a threat to any major world power that annoys him - and if they found the camera in Tibet, they know who his first target is likely to be.

Also consider that Matt's interests are psychology and philosophy. Even without the knowledge (and catchy quotations) study in those fields grants, he could very easily start a cult or similar movement based around his powers, giving him an even bigger reach. Heck, the US government might assume he has the ability to imbue others with his powers. Heck, maybe he actually does.

So yeah, if I were a high-up in the US government, I'd be pouring literally everything I had into both covering up the events of Seattle and capturing or destroying Matt. He's simply way too dangerous to be left alone.

The sequel will be in the point of view from a different group with the same powers.
As Steve led Andrew down to see the cave where the weird space rock thingy was, he mentions how there were other people down there checking it out, but they're gone now. Who's to say they didn't go down into the cave before the main trio did?

The Strange Object the boys found was, at one point, another telekinetic.
One of the other WMGs on this page said something about Matt being able to give others his power, perhaps the Object was the final stage of the evolution of the powers. Eventually, Matt will turn into another Object and bury himself out in the wilderness.

The 'object' gave the boys an alien parasite.
I got the impression that the object they found was either living or contained something living. The parasite takes some nourishment from the boys (maybe from inside their head) while granting them these powers. Mutualism. Why do the boys bleed when they over exert their new powers? Over-exertion causes the parasite pain which causes it (or the boys themselves) to bleed from the nose. Why do the boys sense when the others are in mortal danger? Maybe it's a survival mechanism of the parasite. A psychic connection that fires up to alert the others that they are in danger.