Transformers Rescue Bots/WMG

Cerebus Syndrome will hit the show
It worked for My Little Pony. No guarantee if the syndrome will stick.
 * They're about to introduce Doctor Morocco, the show's first honest-to-goodness villain, this weekend. Furthermore, his plots have been brewing in the background for a while now, and he's voiced by Tim Curry, so depending on how evil he truly is, he may be the one to bring about the aforementioned Cerebus Syndrome.

A Decepticon will show up at some point

 * And he will be a Knight of Cerebus.
 * Perhaps a future plot will revolve around finding one in stasis on Earth, with the objective being to keep him from re-activating?

Rescue Bots is set in the same Continuity as Prime
Optimus has assigned them to work with humans away from the war in hopes that some transformers with a purpose other than combat can survive. Acting as goodwill ambassadors to earth is just a bonus.
 * Confirmed by Jeff Kline himself.

The season finale catastrophe will be caused by Unicron

 * Expanding upon that, the Rescue Bots will be called upon to deal with one of the natural disasters caused by Unicron's awakening.

Bumblebee will be the first character to cross over from Prime to Rescue Bots.
Nicked this theory from Chris McFeely; there will be a future episode wherein another Autobot is called in to give the Rescue Bots some additional support, who turns out to be Bumblebee (whose official design for this series is already very Prime-like). In the corresponding Prime episode that same week, Bumblebee will be absent, with Ratchet or someone else explaining that he's away on a "special mission".
 * Confirmed by the description of episode 18, insofar as Bumblebee being the first Prime character to show up. Prime itself is on hiatus, though, so it's safe to assume there will be no corresponding episode accounting for his absence from Jasper.

Doctor Morocco is in league with MECH.
Even the Wiki thinks this one is a possibility; he mentions that he's selling weapons to a certain client who's seeking out advanced weapons for the purposes of building an army, and who do we know in this continuity who wants that?

Trex is Grimlock.
The other Dinobots have been deactivated and Grimlock has been reprogrammed