I may be way off base on these educated guesses, but I was pretty spot on with most of my predictions on this series, so here goes...
New characters to expect in season 2:
Dreadwing: Well we know this guy is coming, he is voiced by Tony Todd, who played Candyman in the horror franchise of the same name, as well as voicing The Fallen in Transformers Revenge of the Fallen, I predict he will be a seeker type character.
Vector Sigma: Jack was given his key in episode 25, and Ratchet confirmed it was the Key to Vector Sigma in episode 26, so expect this orb who can grant life to machines to show up in season 2
The 13 Primes: Having already been seen in a flashback, I would dare say it is more likely then not that some of them will surface in season 2. personally I expect Alpha Trion, The Fallen, and the legendary weapon maker Solus Prime, though Vector Prime and Prima are also good candidates to surface.
Ironhide: The Transformers Prime toyline has an Ironhide figure scheduled for release in wave 2 in January, I'd call this a good indication of the next major Autobot member.
Quintessons: Having been mentioned in passing in a flashback, this malevolent five-faced is a long shot to appear, but one I hope will.
David Kaye's character: The voice of Megatron 2 will be taking on a role in season 2, will it be Megatron 2? Probably not, but I look forward to finding out who he will play.
Predictions on pre-existing characters:
Starscream will join the Autobots.
Airachnid will lose her status as second in command of the Decepticons following her attempt to abandon Megatron.
Optimus will have his memories restored by Vector Sigma.
Soundwave will speak...
Wheeljack will return...
Arcee will lead in Optimus Prime's absence.
That's all I have for now, we'll see what pans out when season 2 starts next month