I have some minor gripes with the upgrading window. I haven't worked with RPGM for long enough to understand all the intricacies and I sure as hell haven't messed around with plugins for long enough, but the way the upgrading window just dumps all the options on you off-the-bat instead of simply proving you with currently available options is a bit overwhelming for me as a player. I know that you are aware of it, because the in-game character goes with a short meta-commentary on that, so there must be some reason why you left it as it is for now. Even the sheer amount confusion it gives aside, it's also a bit spoilery. With items you can somewhat overlook that, but when it comes to upgrading blessings, you kind of find out about many characters you haven't even interacted with. Sure, you might have not met them and probably don't know anything about them but it takes away a bit of that... magic of discovery, I suppose? Just rubs me the wrong way, personally.
Also, maybe it's just my imagination because I haven't bothered making any direct comparisons later on in the gallery yet, but it feels like the H-scenes seem to be becoming shorter, narrative-wise, compared to those in the first parts of the game. Too, it's not all that critical, I can totally understand that it's becoming harder and harder with providing the scenes with the same amount of "juice" as before due to the sheer amount of characters involved, plus it's something that can be improved upon later on when the game's foundation is totally finished.
That's all I can say for now off the top of my mind.