I believe the great villain of the show will be whom we least imagine ... I bet on Lena Luthor.
I'm rather hoping it isn't Lena. I don't like revolving door characters (think Malcolm Merlyn...good to bad to good to bad to...).
Also they set up Lena as a red herring so frequently and then finally vindicated her. I thought that was good because it would be so cliche to have her as bad.
But going along the least imagine concept you put forth, maybe it's Mon-El (I mean it better not be because he's such a great teammate and I want him in future seasons)
In the year 2166, my planet Krypton was dying. I returned with only one goal, but my pod got knocked off course, and by the time I got here, an accident made me the impossible.....