Want to give my 2 cents to this
Yes, the game is fairly complicated and I generally dont mind because I much prefer that over a game that is mostly linear and maybe gives you the choice if you want to date a certain girl or opt into a certain fetish and thats it. As you said, you cant have your choices matter and all content being easily available to everyone, regardless of choices made, at the same time.
However, there are a few ideas to maybe make it a little easier on players.
1) would be to periodically give players a summary of the choices they made. Lots of games already do this, for example Radiant at the end of each chapter tells you how many stat values you currently have, how the game interprets your choices (are you good, evil, horny?) and what crucial choices you made this chapter (did you visit character x or not?). Something like this might help.
2) Having an official walkthrough that explains all the different routes and variables in a flowchart that releases at the same time as the update does. You could maybe find a volunteer to write it for you and you let them playtest the alpha version to write it.
3) putting most or all of the content into the full harem route. I believe the full harem route is what most players prefer anyways (but I dont know, maybe I am projecting from myself here). You could of course argue that this reduces the impact of choices, but I believe you can achieve a great deal of route divergence while still having a full harem on all of them. For example how you respond to Eve the first time you meet her could set her on a romance/domination/corruption path, so your choices would matter without having to reject her. Currently a lot of the content in SSP requires you to reject girls or even letting them die in one case.
But again, those are just ideas. I think the game design as is, is already better than many other games that are 90% linear.