Personally, I'm surprised no one's come up with the first one yet.
1. G1. In TFA, the seekers are all basically clones of Starscream. In G1, Shockwave successfully clones Starscream, creating Sunstorm. What if all G1 seekers are clones of Starscream? The reason why Starscream doesn't have an 'ability' like the others (teleportation, sonic boom, etc) is he's the original and didn't have any speciality to begin with. Those were added onto the clones.
Two plot bunnies for this plot rabbit; i, Starscream knows they're all clones and that's why he's Air commander
ii, Starscream crashed in the ice as well as Skyfire, and back on Cybertron Shockwave takes the blueprints of the only seeker and clones Starscream as a perfect replicer, only with more vindictiveness and treachery. Vorns later, when Skyfire has been found the shuttle moodily goes to contemplate where he crashed, thinking about how his friend has changed. To his shock, he finds someone very familiar in the ice... in the origional tetra-jet formatting and badly damaged, Starscream is there. With no decepticon sigils.
2. TFA. Vorns before the great war began, Nova Prime and Megatron ruled together as Prime and Lord Protector. Megatron grew cruel with power, and in his desperation, Nova created a spark from himself, his bondmate Megatron, and the allspark. However, he was only able to hide it with a name, no indication of who the creators were or even the faction, before Megatron started the war. The only one who knew was Alpha Trion, who was hiding the spark. In the confusion of the war, he lost the spark, and thought it dead.
After the war, some mechs find a spark container holding a steady spark with one name on the side - Optimus.
3. TFA. On Cybertron, Oil Slick starts spreading the cosmic rust virus. No one knows a cure, and the elite guard can't find a way to combat it. Just when all hope is lost, Perceptor/Wheeljack remembers their old friend Ratchet mentioned something about when he was younger creating a cure for the cosmic rust virus. Oil Slick unfortunately around this time finds out Ratchet, who foiled him once before by creating the antidote, is still alive. The race to earth is on.
and three crack bunnies, just because I can.
a. Optimus Prime (G1) meet Optimus Prime (TFA). See G1 Prime teach TFA Prime. See TFA Prime become hero-worshipping of G1 Prime. See them accidently meet under the mistletow and all the G1 autobots whip out cameras.
b. BW Depth Charge and Cheetor start going out. Each of their 'dates' is sabotaged by a different Maximal as the maximals strive to protect Cheetor.
c. We've all seen G1 Starscream switch places with another Starscream... what about G1 Brawn and RID X-Brawn swapping around? Or G1 Inferno and BW Inferno?