Penguin, Harvey, Lady Arkham, Freeze, Bane, Harley, Waller, and John Doe are all still out there. Do you guys see many of these characters returning?
I think John Doe will definetely come back, he was the focus (and the best part if we're being honest) of the entirety of TEW.
I would really like to see Harvey come back too. His story was never really given a proper conclusion, and I loved Telltales take on him.
Penguin, without a doubt.
Episode 5 had the newsfeed talking about him failing to get permission to leave Blackgate Prison. I doubt that Telltale added that at the very end of the season without thinking about him returning in the future, it's just too obvious.
And besides, he is the ideal villain for a small return. Harvey and Lady Arkham are affected by some choices that could mean extra work, and they are also much more relevant to Bruce and the plot from season one. Cobblepot, on the other hand, hates you no matter what you do, and he isn't that important as a character. He works just fine as a secondary villain that doesn't steal the spotlight.
My bet is on penguin and Harvey/Two face. Definitely not Lady Arkham. Maybe joker will get some cameos but he won't have a big role due to the different jokers we can have.
I think Harley, Mr.Freeze, and Harvey should return because they all were amazing characters and Mr.Freeze was defeated pretty easily by Batman. In my game Harley is still working with Waller so there is a chance that she will return.
I want Oz to return so badly. He was my favorite character for the whole season and his conclusion was really disappointing and unsatisfying. Such an awesome character and I want to see him in the spotlight.
If you read the newspaper on the Batcomputer, there is information about Two Face and Penguin that hints on their return.
Penguin is currently at Blackgate where he is apperently beloved by the guards as the "role model" for prisoners. He will likely use this leverage to his advantage and get out somehow.
Two Face is going nuts and wants to defend/represent himself at court rather then having a lawyer . This means that he will likely be send to Arkham rather then Blackgate where.....John is.
Freeze Bane Harley Waller and Joker I don't think will be back in the next season seeing as how they were in the last season.
Harvey and Lady Arkham I wouldn't mind seeing come back in season 3
The reason being while both of them would want to get their revenge on Batman. I can imagine Harvey at least would want to get revenge on Lady Arkham as well due to the fact that while it can be argued that Harvey's disfigurement (if you chose to save Catwoman) is Batman's fault. If you chose to save Harvey then his mental break down is the fault of Lady Arkham and her drugs.
There is also the added bonus of Lady Arkham aka Vicki Vale potentially knowing Batman's secret (if you chose to remove your cowl) and how she could use that against Bruce/Batman and whether Bruce has given up Batman or even if he hasn't the threat of Vicki revealing that secret would be a major problem for him.
As for Penguin I can only see him coming back if he is with Lady Arkham due to the fact he doesn't strike me as a 'big bad' of the season kind of baddie he is more the side kick.