The problem with this sprawling framework is that it creates the expectation of massive amounts of additional work just to finish off everything. Reducing the scope of the game would help with that.
The biggest example of that is the 'private room' and 'exhibition' section of the bordello. Those are completely unnecessary, because they're already covered elsewhere, either in the cells or at the Glamour Slam. There's only so many ways you can draw or animate sexual acts, and multiplying that times 6 jobs times 12 heroes is going to result in tedium and repetitive work.
If he wanted to retain the existing bordello framework, he could change the second two categories to 'date' and 'orgy.' Date would be a completely non-sexual night out with a hero, so only one image would need to be created for each hero. Believe it or not, this is kinky and sexy in it's own way. It would need to be the final category, since the mental control would be the most complex. The orgy category would also be just one single image, and he could limit the orgies to specific groupings, so he only has to make 4 images total. Additional groupings would be 'maybes' for later.
The outfit categories need to be drastically reduced. 2 non-nudes is good enough for nearly everyone. This is because they need to be redone for every alternate scene. All of Chesire's and Artemis's outfits need to be redraw for the fingering scene, that's too much work, especially if there's a different pose required due to a skirt or whatever. Don't get me wrong, I love all that detail, but it should only be done if he feels like it.
Everyone wants penetration in the cells, but I think it would be better to limit things to where they are now, and only include actual sex when its a good concept. As I mentioned, the real 'goal' of every cell capture should be to attain some specific information, resource, or material from each girl. For example, for Audrey, the goal would obviously be to attain some political favor from Savage. The goal from Lois would be to get a fresh sample of Clark's DNA. The goal from Starfire and Blackfire would be attaining some ability like radiation absorption , etc. I'm not sure exactly what form 'upgrade 3' is supposed to take, whether it's sexual, behavioral, emotional, or something else, but it doesn't have to be tied to the goal of the character. In line with the nature of the story, which seems to be placing cocky women into a state of sexual submission, I think a variety of effects would be better than the consistency of "upgrade 2"
I think Lex should actually 'win' and conquer the Justice League and the world, since these women are obviously getting slowly convinced that he's their master. This requires a bold narrative, but it's not hard to begin to piece it together, you just need a specific goal for each 'cell' occupant.
I think threat 'works' as it is now, since it creates a false sense of tension, but once the game has been underway for a while, it can develop a real meaning. If he removed the ability to preemptively remove threat by hiring a villain, then threat growth would have meaning again, because you would know that something 'bad' will happen once threat hits the cap. But as long as you had a powerful villain(s) on the payroll when this happens, you'll (usually) be able to use them to distract the (male) hero and threat will be reduced, in whole or part. But hitting this threat cap will also carry opportunities, like events or captures that can only take place at maximum or high threat. Lois and Wonder Woman could be a high-threat capture only. Henchwomen could then be given bonuses that affect the types of events that happen when threat hits maximum. (and other types of bonuses) For example, Galatea could slow down threat growth to a trickle when it's near the cap because no one is dumb enough to fight her without a plan. There's a lot you can do with this, such as having better heist options when threat is low.
I could keep going about these things, but I honestly don't think the game has any big problems. The quality of the art and writing is far better than I was expecting. Looking forward to whatever is next.