I mean, I didn't think it was obvious she was evil as much as it was obvious that she would end up going mad because the show makes a huge deal of reminding us that Targaryens eventually go mad due to inbreeding. I think it was like Chekov's Gun, they wouldn't keep showing off this information if it wasn't going to become important.
I think they planted the seeds for this ending early on, but absolutely fucked up and didn't do anything to nurture the seeds after planting.