Lin is the first character you meet and Autumn is the newest to be introduced, so of course there will be a difference, that will always exist. Some events could be reorganized as well, because while characters like Ashley have a high number of events, a lot of them are incredibly short and probably aren't worth calling a story event anymore. Those will be remade.
v0.16 is actually the update I've decided to do some balancing in. Lin and Ashley won't be getting any story events in v0.16, while Autumn will get 3 story events, and F&E and Android will get 2. (Rest get 1). This won't entirely fix the level gap, but the level number isn't as important when some of those early story events for Ashley last 1 minute.
There's tons of meaningful player choices in Harem Hotel. I think you're confusing that with branching story paths, which I will never include. It would completely detract from the story I'm trying to tell and essentially make it impossible to finish the game. Even if there were 100 of me I wouldn't do it though because I'm not trying to make a story of all stories, I'm just trying to tell one.