I don't have an issue with her. If I can accept anyone coming before Superman its Diana. I'll always have a problem with the rest of the JSA being before him though. It never felt right to me for the 30 years it was canon till the reboot, and it still doesn't feel right now that they've gone back. It never will with me, but at the same time I know now that's just the way this regime likes it and are comfortable with.
Overall timeline though, I still don't feel any better about the situation. I just have no interest into this all building to a "present day" where my characters are in their 60s. I mean, for Superman himself in a vacuum it wouldn't matter, but it matters for most everyone else. Including Superman's supporting cast, most notably his freaking wife. I'm not seeing it working at all. I know there's the historical portion that would have the characters in more classic roles, but what happens when that history is told to the degree they wish to tell it?