You bring up a few great points there. One of the shortcomings of the Ren'py platform is that, out of the box, it's basically set up to be a choose-your-own-adventure style visual novel creator. Thankfully, they built it on top of one of the easiest scripting languages out there (Python), and designed it with creator control in mind. That said, it's not
terribly difficult to make all of the nuance happen
in theory. All it really takes is a whiteboard, several hundred sticky notes, and a lot of alcohol (an essential research and development tool). The issues really come in (and I'm sure
WillTylor and
strenif will back me up here) when you actually have to create
every single fucking render required for those nuanced scenes happen. It's an impossible tradeoff. I'm sure that Will has a few thousand ideas that he wants to throw into the game, but when you try to go from concept to Lauren, Mandy, and the MC having a three-way while Aunt Cami is standing in the doorway and Matt is peeping through the window, along with everything that led up to it,
and the aftermath, you're in for 50+ renders that might take ten minutes or a couple hours each, an overnight animation or two, and you've forgotten whether the cat shit in the box or if it was you because you've been too busy trying to stuff an ice block into your computer to cool it down.
That's actually one of the things I like about AFV: all of the side adventures have room for expansion, and Ren'py is fairly easy to work with in terms of going back and adding new content. For example, the "night games" with Mandy and Lauren can be expanded (nudge nudge, wink wink) at any point in further development. It adds extra content to the game without impacting the primary storyline. The same can be said for the cosplay, Aunt Cami housework, Agent Diaz, Jacky, etc. side bits. And still, the primary story is essentially unaffected. It's a hard thing to pull off, however, if you've got reactions/scenarios that may affect interpersonal relationships down the line. That's a lot of variables to track, and differences that need to be addressed if you're going to keep your game making sense.
I think that Will has managed to handle that fairly well with the Affection/Libido/Submission/Anger stats on the girls which will lock you out of some story-driving/repeatable scenes if they're not at the right values, and the prerequisites for some storyline progression events, such as the student election.
I've gotten a bit off topic, I think, but really what I wanted to get at is that (pretty much) every game (of any kind) is a narrative that takes the player through a core story, so I absolutely agree with you that it should always come back to the main branch so that there's progress of some kind, leading toward a goal (whatever that might be
banging the entire cheerleading squad in the showers), but getting all of the nuances of possibility into a game is bloody fucking hard. As a fledgling AVN developer, myself, even with a background in programming, game design/development, and adapting a 600 page novel that I've already written, it's not exactly a walk in the park. Every time a what if comes up, it costs me hours and hours of scene setup, set dressing, and rendering time. I recently lost two days to a stray thought of "well...what would've happened if he decided to open that door, instead?"
Dynamic characters are great. As a writer, I love it when one of them goes haring off to do something that I totally didn't have planned. When I wake up the next day and realize that I actually have to figure out the myriad consequences of an errant pen stroke, I usually want to take myself out into the woods and live with the squirrels so that they might come to worship me as their sovereign master and nest in my wilderness beard.
Variations in the storyline take a lot of time when we have to subjugate technology into bringing our concepts to pixelated life, and AFV has done it better than most. Give them time, head over to SS and pledge a subscription. The more people that support it, the faster it will move along, and the more that they'll be able to start wedging into the game.
On that note, I have either had too much to drink, or not enough, so I'll be heading off to fix it, one way or another 
P.S. Apologies for the rambling. Please reference the above sentence.