I'm honestly not too familiar with the franchise. I thought that maybe each individual game might have one or two storyforms, depending on your choices?
I'm most familiar with Final Fantasy X, and I agree that it probably has the strongest story form.
Steins;Gate is great. I've seen the Anime and only skimmed over the visual novel, but as far as I know, the visual novel is only more detailed in the route the Anime takes. Who Main Character and Influence Character are is pretty clear, I think, but I don't know if their throughlines are developed enough? And I'm worried that the real story doesn't actually start until Episode 13 or so, where Goal, Stakes and Limit are established.
Have you heard about Narcissu? It clearly has the subjective throughlines, though I'm not sure how challenging the Influence Character is, let alone how strong the overall story might be.
I find Katawa Shoujo interesting on a meta-level. It is fascinating to me how it even came to exist. Something to keep in mind: each route was written by a different author. So the quality is rather inconsistent. And while I would not call any of these routes 'great' by any means, they are all way better than you would expect. Rin and Hanako's route especially.
While each route would have its own storyform, I think only one or two be something close to a complete story. Most of them don't have a clear Overall story, and I have trouble finding any story limit. In addition, how well defined the Main Character is depends on the route as well. Again, Rin and Hanako's route are probably the strongest in this respect, followed by Lilly and Emi, and lastly Shizune.
... Yeah, I've read through this thing recently. Unfortunately, like many Visual Novels, it takes a while to complete a route, 4-9 hours depending on how fast you read and such. Although its wiki describes the routes in enough detail that one might be able to determine the storyform from that? I tried, but I couldn't really decide.
Yeah, later Point-and-Click Adventures are generally more plot-centric (as opposed to being just about the puzzles), though I'm certain that most of them have neither Influence Character nor Relationship throughlines. Gemine Rue could work though. It's been a while since I played it.
Now that I think about it, Telltale's The Walking Dead (with Lee and Clementine as MC and IC) and The Wolf Among Us might be complete stories.
In this case I think looking at the three/four play styles (genocide, no-mercy, 'normal', true/pacifist) individually would lead to better results. I could imagine the pacifist route having its throughlines like this: OS Situation (Monsters are stuck underground and want to get out), MC Manipulation (dealing with monsters through persuasion of some kind), IC Activities (monsters consistently attack you), RS Fixed Attitude (humans/monsters are evil), with MC Resolve Steadfast and IC Resolve Change.
So, here are the games I'm most familiar with / wouldn't have to replay/rewatch to try and figure out a storyform: The Last of Us, The Walking Dead, Katawa Shoujo, Steins;Gate, Undertale (Pacifist), Final Fantasy X, Silent Hill 2