What I really want to see happen mostly revolves around Optimus/Orion Pax and his successor.
Firstly, I do NOT want the Key to Vector Sigma to be the MacGuffin that restores Optimus's memories. I want it to have some other, more mysterious and deeper purpose than the obvious. After all, the creators could have put it in there as a Red Herring for us to all speculate how it would bring Optimus back, when it could instead be for some other purpose just to throw us off.
With that said, I honestly don't want Orion Pax to get his memories back. That's right, I don't want the same old Optimus Prime back. Why? Because he is so BORING a character. I swear, he is the worst character of this whole show, as his complete stoicism is just so overbearing. His only good personality trait is his high regard for the the Autobot Code, but lacking a wide enough range of emotion severely cripples his character. So, it pleases me to see the youthful, aspiring dreamer that is Orion Pax brought back from the ancient past. He was SO much more appealing than he was as Optimus.
What I'd like instead would be for him to come to find more favor with Autobots than the Decepticons all on his volition. Something like how BW Silverbolt willingly chose to join the Maximals after preferring their good nature over the Predacons' harshness. After all, Orion Pax was anything but stupid, so he should be able to see right through Megatron's act relatively quickly. And afterward, have Optimus/Orion then begin a long process of trying to grow back into the leader he once was, retraining himself to be a Prime. But instead of him becoming the same as he was before, have him become an even better leader and greater character than ever before (one who can show EMOTION). It would be a great chance to develop him from a youthful, relatable character into the role model that we all know and love (a la Animated Optimus).
And with him not getting his memories back, that leads me to who would be his replacement as Autobot Leader. Seeing what went on in the season 1 finale, I feel that there is only one logical choice. Since Optimus personally gave him the Key to Vector Sigma, I want Jack to take command (and maybe have Ratchet and/or Arcee as his advisor[s]). After all, it wouldn't be the first time that a human was Commander of the Autobots, and it would be an interesting take on Jack's character, giving him more responsibility and allowing him to grow and mature even further.
I mean, Optimus handing him the Key was practically an act of Optimus choosing Jack to be his successor. And, it makes sense since Ratchet compared Jack to what Optimus was like in his own youth. Jack taking command would be no different than when Optimus himself became Prime. He, as Orion Pax, was a nobody. A young data clerk with dreams of a brighter tomorrow and no real combat experience whatsoever. He got the job because of destiny. Bearing the Matrix, Optimus may have sensed some potential within Jack just as Alpha Trion, Halogen, the rest of the High Council, and the Core of Cybertron (Primus) himself sensed potential in Orion.