I perhaps wasn’t clear enough, but I think there mostly isn’t a better way on mobile right now, and so I don’t think the bugs in Marbles are your fault.
I think the platform has (mostly) failed you. The question is how best to support you (and other authors) in the future.
For example, if there were an easy-to-use Inform extension for supporting dark mode (which there isn’t right now), I’d recommend that authors use that instead of just hardcoding colors.
In the short term, I think the best thing to do is to is to give the <input> a clear border, which will hopefully make it clear enough where the player should tap to begin typing.
(Also, I think the interpreters’ defaults are bad here. IMO, Quixe/Glulxe should render the input line in its own window pane, outside the main transcript.)
In the long term, Quest displays a “Continue…” hyperlink whenever it expects the player to press a key; you can tap the hyperlink (which disappears when you click it) to make the game progress. I think that would require Glk to support a feature like that.
re: Flexible Windows by Jon Ingold, I’m hazy on what’s going on there. Has nobody gotten around to re-implementing it for Inform 7 v10? The underlying Glk API is still accessible. You can still write I6 code in Inform 7 v10, so it seems like it should be straightforward to re-implement Flexible Windows without a lot of fuss…?
FWIW, I think a Cairn-like or Quest-like UI would need more than just the features offered in the old Inform 7 Flexible Windows. Even with those features, you couldn’t create a window that the user can drag/close/reposition, or a horizontally scrolling window (occupying a minimum of vertical space on mobile), or a side-pane window that automatically converts to a horizontally scrolling window on mobile. That stuff would require new features in Glk.
Parchment and Quixe support style hints by default, and don’t offer any settings UI for players to select color schemes/fonts, or to decide whether to override author stylehints. If the author selects a light color scheme but you’d prefer a dark one, in HTML, you’re currently stuck.