Based on the newest episode of Gotham, "A Dead Man Feels No Cold" (Aired on 3/7/16), I have a great theory about the events and roles of characters. I have read on multiple threads about the flaws in the events of Gotham and this theory may explain all of them. (WARNING: Contains spoilers to the episode listed above.)
First, when Mr. Freeze killed himself, it made zero sense to me. That, at first was a major flaw in the story line of Batman. How could Batman fight him if he was dead. Later it shows him alive in Indian Hill after the mutation of his cells happened. Thus, my first thought was completely cancelled out and I started thinking. Then, when Hugo Strange is staring intently into a room filled with vats with people who are "dead". The first thing that catches our eyes is the very first vat containing Theo Galavan.
The next tank over is, if you didn't catch, Jerome! This brings back the whole, Jerome is the Joker theory. There is several other people in these tanks. Also in a previous episode we got a peek at some others in different tanks, one who oddly resembled Fish Mooney. So in all, we may have met most of the major villains already and disregarded it due to other events A.K.A. death.
To further this theory, I believe Hugo Strange is going to bring back all of the old villains we were led to believe were dead using cryogenics. I believe they are going to bring back all of the following characters: Jerome Valeska, Theo Galavan, Gerald Crane, possibly Stan Potolsky, and Fish Mooney. Jada Pinkett Smith already confirmed she was coming back to Gotham!
Please tell me your thoughts!