Jem/WMG

Rio knows Jerrica is Jem
Ok. This sounds like a Wall Banger, but I have a believe that Rio's crush on Jem is a fraud to protect Jerrica Benton from harm. His melted core-like temper is only a short-term one. Ok, about the dairy from "Out of Past" in which Emmett said it took two weeks for Jem to thaw out Rio from a prank she pull using Eric Raymond. In the last scene of "Out of Past" Rio stated that he forgot that one. He said in "Glitter N' Gold", that Rio states that he gets mad, but he stills care.
 * Word of God is that at one point Christy Marx actually toyed with the idea that Rio knew all along but didn't go through with it.

"The Laugh Last" video the Misfits saw was Video's April Fool's Day joke. The real "The Last Laugh" video was reveal later.
This explains who was behind the video clips. Now, you going to said the Starlight Girls did it. I believe they really put together the real "Last Laugh" video, which wasn't the one we saw.

Rio and Jerrica had a polyamorous relationship.
Rio really didn't know Jem was Jerrica (or else suspected it on a subconscious level but was in deep denial), and that he and Jerrica had a polyamorous relationship. Fandom tends to give him hell and call him a hypocrite considering he hates liars but is "cheating" on Jerrica with Jem, but the problem with calling Rio a cheater is that not once on the show has he ever lied about seeing Jem or about his feelings toward "either" woman. He openly gushes about Jem to Jerrica, but when Jerrica takes issue with it, it's never that he's talking about another woman to her, it's that she feels like she's in Jem's shadow (that was the whole point of "Who Is He Kissing", Jerrica's insecurities about his feelings for her). Rio's also declared his love for both on any number of occasions without any weirdness from anyone. One could argue that Jerrica never called him on the "cheating" because she was afraid she'd inadvertently out herself, but that doesn't explain why Rio felt so comfortable talking about his feelings about Jem to Jerrica. The poly theory also neatly skirts the number one problem with the "Rio knew Jem was Jerrica all along" theories, which is that Rio's Berserk Button is fraud/deception; polyamory is about open, honest communication between partners. It would explain why no one in universe seemed to bring up the fact that he was ostensibly dating two women at once.
 * Kimber does bring the fact Rio is dating two women on occasion. However, this mainly shows her to be Rio's foil. Rio and Kimber both date multiple people, but Kimber tries to deceive the guys she's dating whereas Rio is honest about his relationships.

Jerrica has Dissociative Identity Disorder, and Jem was an alter that came to subsume her personality.
At some point, the strain of keeping up the Jem persona combined with the pressures of running Starlight Music and the foundation, plus managing her personal relationships and fending off Eric Raymond's schemes eventually grew too much for Jerrica and she cracked, developing DID, with Jem as a full-blown alternate persona. Note that from a certain point towards the end of Season 2, Jerrica starts consistently referring to Jem in the third person even around the Holograms and Synergy and during occasions where it makes no sense to do so (ie no scheduling conflicts), and does so for the entirety of Season 3. You could argue that because she's been lying for so long it's just second nature, but even her own sister refers to Jem as a separate person to her. Alternately, the trauma of losing her mother was what triggered it, the Jem alter was created then, and it grew stronger as Jerrica slowly started losing her mind.

Techrat is a Time Lord.
See here.

Hasbro is gearing up for a Jem revival
After the success of G.I. Joe: Renegades, Transformers Prime, and My Little Pony Friendship Is Magic they'd be fools not to... and notice that The Hub started airing G1 Transformers and GI Joe a little while before their respective revivals started up. Could there be a pattern? I hope so.
 * It would probably be Animesque and deal with Jem's daughter, maybe.

Jerrica doesn't press charge against the misfits because it wouldn't do any good.
Jem and the Holograms takes place in the same universe as G.I. Joe. In an early episode of G.I. Joe, Cobra Commander is arrested and place in a supposedly inescapable prison. He immediately escape. Any prison the Misfits would be placed in would have much weaker security. It probably wouldn't even have locks.