You can have a well written story and characters without branching paths and forced choices. People have been making them for thousands of years. In fact DC and sploosh have done it as well on multiple occasions. I mean credit to their writing that side characters like Grace have any character or romantic interest at all. In most of these games you wouldn't even remember her name. In fact I'd argue that their writing has gotten immeasurably better since they did away with the choices and started focusing more on the routes' lead characters. I mean take the Mia route or the Mrs. Johnson route for example: I almost forgot they exist personally and no one ever argues for their characters. But the Roxy Route? I remember. The Eve route? I remember. The Jenny? The Debbie? The Dianne? The main? Less so, but still I still remember them more than I remember Mia's mom or the chubby nerd girl from those routes. And neither of those choices ended up feeling good or fleshed out or meaningful in any way anyway. The choices in the game so far just don't have a good track record. Better to do away with them completely or just shoehorn them in at the very end in a way that you can just save and reload to get all the endings.
Ultimately it's all about variety. And as said, you can hardly have a really nice and deep "classical" romance arc if the girls goes "ah, whatever, I don't care whome else MC fucks" right after that. These choices enable certain plotlines which else just aren't credible.
When it comes to Mia and Mrs. Johnson, it's just the case that they aren't reworked yet and as such simply lack the depth of let's say Roxxy's or Eve's story (these where 50 to 60 day updates instead of the 120 days+ we get nowadays). In fact both of these stories are so old, that they were actually written by DC himself before Sploosh even joined the team. So it's not really a surprise that nothing is fleshed out. That's gonig to change once they are reworked. As of now it looks like the choices will stay but in a slightly different way (at least that's what DC said). Next to that Judith's story will probably get a choice, too.
Edit: What I mean by that is that you can just write better and more unique stories. I actually liked things like bringing Helen and Harold back together or getting Erik a girlfriend. It's just something you don't see in that many other games and it actually adds a really nice touch to these stories.
But yeah, in some sense these old stories probably incapsulate quite a bit more what SS was supposed to be back when DC wrote everything by himself and it certainly wasn't a classical harem game.