The Administrator is...
They will eventually do Every Trope on the Echo Chamber pageWhich will eventually result in more tropes on their page which they will also cover.
The season finale trope will be...
The crew will eventually encounter The Advertisement Server
Dana's Freudian ExcuseShe was teased for being so nerdy and shy as a kid, so she now defends herself with cutting-edge sarcasm and irony.
They will soon do Trope Tropes
Zack is a Time LordHow else could he get footage of the same scene from several angles with one camera? He obviously teleports somewhere else just a few seconds previously, and gets the shot. Also it's highly unbelievable that Tom would have gone this long, having made so many death threats against Zack, without killing him. It is therefore not unreasonable to assume that he has, and Zack has merely kept regenerating. The reason he is kept off camera is to hide this fact from us.
A future episode will be about Murder the Hypotenuse.In which Shannon tries to kill Dana. She fails, obviously.
At least one of them will become Genre Savvy.Realising that they live out whatever trope is the video's subject, they try to stop Tom's choices if they would suffer for it - "No, you can't do Broke Episode. I'd rather eat this week." Most likely Dana, because she's in front of the camera and Tom's foil.
We will see Zack's brother appear in front of the camera in a future episode.According to the YouTube channel (Word of God?), his name is Dave and he is the Visible Boom Mic operator. And you were supposed to see him.
Tom is plotting to kill Shannon off for realThe way he put away his laptop quickly when Shannon appears? Nah, that isn't him doing some editing. Also he might like her for two reasons, but eventually she will get in the way of Tom's wishes for Total Trope Domination
Porn Girl is actually a spy from a rival site or TV Tropes rival vloggerShe is trying to put Tom off so that he gives up on making vlogs, hence her sudden break up with him.
They will do Hilariously Abusive Childhood.Or rather, Tom wants to. Dana objects, saying abusive childhoods are never funny, and to illustrate the trope, Zack's dad shows up.
Echo Chamber is actually a documentary focusing on 3 students at Carnegie MellonTom is really a Jerk. Dana really is a Dead Pan Snarker and Zack really is a Strange Guy who films everything. They say it's a Web Video show to cover up the Truth!
Shannon and Zack will have a relationshipThat stinger from the Did You Think I Can't Feel? video can be interpreted as such, what with Shannon's smirk.
The whole series is actually a computer generated Lotus-Eater Machine/Ontological Mystery/Psychological Torment Zone (Delete as appropriate)The Administrator generated it all in Tom's mind in an attempt to see if he is indeed capable of creating Trope Vlogs in a set of bizarre/confusing/stressful situations. That way when Tom wakes up the Administrator has a good idea if the quality of the vlogs is consistent enough to be featured on the TV Tropes site.
Zack is Mr. Administrator.This will be revealed in the Trope-Of-The-Week video for Obfuscating Stupidity.
Mr. Administrator's father is the (or one of the) creator(s) of TV Tropes.Mr. Administrator said that he sympathizes with Zack, and Zack's dad is forcing him into a life he doesn't want. So Mr. Administrator's dad is forcing him to carry on the family tradition. Puppetmaster announcement comes out at the same time as the last episode? Rather suspicious if you ask me...
True Companions will have an episodeFollowing the logic of the above WMG, the renaming of Nakama was also on the bulletin some moments prior to the finale. The theory of why could be because the creators didn't want Echo Chamber to have Gratuitous Japanese for fear of being called a weeaboo.
Zack is Obfuscating Stupidity as part of Mr. Administrator's assignment.He wasn't being stupid at the end of Mysterious Employer, though— he needed to pee and genuinely wanted to know where the bathroom was!
The Series Finale will be Apocalyptic Log.Or Series Fauxnale, if they don't want to go out on a Downer Ending.
Ace is Tom's Big Little Brother.Always Someone Better? Check. Looks younger? Check, at least in my opinion. Gets more approval from authority figure (parents/Mr. Administrator)? Check. Tom didn't mention it because he's already upset enough about being overshadowed by this guy. He doesn't need people knowing they're related, too.
Season 2 will end with  cancelledTom, Dana, and Zack will somehow get the show cancelled but due to feeling bad for Ace and everyone involved, they decide to let them become a part of Echo Chamber, resulting in a much better show that Mr. Administrator loves.
2x11 (or maybe 2x10) will be Broken Ace.Stephen's character arc will end before the finale.
Umphrey Bridgeport will be back.Given The Reveal in his episode's Stinger, it would be interesting to see him return. One possibility: since Mr. Administrator didn't pay him for his work, maybe he'll tell our heroes the truth and become a Sixth Ranger.
The second-last episode ever will be TV Tropes Will Ruin Your LifeIt will be the one and only time that a meta-trope is used as the title for an episode, and will show the break-down of all the main characters - including Mr Administrator, whose motivations will be known by then. The last episode will then show them finally breaking free of the curse of TV Tropes ... or do they?
Mr. Administrator is playing both sides—and he's actually Good All Along.As of 2.11, it's been shown that he's an admin for The Other Wiki. There's no reason he can't administrate both TV Tropes and Wikipedia. Mr. Administrator is trying to bridge the gap between the two wikis, for whatever reason.
Uncle Bill, Zack and Dave's uncle, is a Manchild because of Mark taking his Big Brother Instinct way too far in their childhood.Mark seems more mature than Bill, and seems to have a bad view of little brothers, showed in episode 2x9. But in episode 2x11, he shows real care for Zack. So probably Mark overprotected Bill from the outside world as he does now with Zack, resulting in both being ManchildS.
Jimmy Wales and Fast Eddie will have a wrestling match in one episode.After seeing how their shows rival each other and finding out that Mr Administrator is interfering in both shows, they'll agree to fight it out between themselves. It'll be as "successful" as the match between Gregorio and Donnagon at the end of Spy Kids 2, and Dave will have to prod them with the boom mic once they're so tangled they can't move. At the end, Gaelyn and Zack will ask them to do it again to get different camera angles.
Administrator 23-09-12-12 is/was the admin for  and 23-01-12-12 is/was the admin of Echo Chamber. 20-08-05-00 and 06-01-12-12 were in charge of two unintroduced, but now defunct webshows that may show up in a later season....or something like that.
Something is going to happen on 23-09-12.The Mr Administrator we know from the show is revealed to have 23-09-12-12 as his serial number. This could be an allusion to September 23rd later this year. Perhaps that's when the third season will start?
Mister Administrator is a split personality, possibly for one of the Main Cast
The wobbly disintegration effect is Zach's Wobbly monsterHe probably saw Administrator Prime using it when he and it freaked him out
Gurt The Lime Man will cameo in Season ThreeThe ARG is already part of Echo Chamber's universe and considering how much of a Memetic Badass Gurt is, he needs to cameo. Plus Tom sorta confirmed his cameo on Twitter by claiming he will have Gurt cameo if fans retweet his tweet about requesting people to watch Echo Chamber, which they have.