I think it ultimately has to be build up for Jay going bad, but that doesn't excuse how hard Bendix is undercut. One could be forgiven for not even remembering he's the villain. Even if he's just a means to an end, Bendix's prime objective should be opening up a new side of the DCU and Superman world. There should be dark room meetings with Bendix and world leaders. We should be seeing first hand how he's turning these people into weapons. Jay's rage and unresolved trauma should be at the forefront since we literally just found out that he was experimented on by Bendix last issue. The scale of this book should feel global. We should be talking geopolitics more than sitting down for a meal at Kent farm.
A Superman who deal with real social and political issues in the DCU should be such a fun book to write. You're basically writing a high concept political thriller. Averted assassination attempts, Superman having to toe the line between the rule of law and what's right, classic villains recontextualized as hired guns for big corporations, trying to get bills passed by saving kidnaped government officials, and so on.
Also, give Jon a damn supporting cast rather than just promoting your original characters from other books. That shit was tacky.