Thanks! I'd originally intended for Sequence I to be a bit less linear—the VR conversation was originally supposed to be an actual NPC conversation instead of just a cut scene, the airlock door was supposed to be actually openable instead of a prop, the door opening was supposed to be puzzle with a computer connector and grease necessary to get the capability to unlock it, the terminal was supposed to have news reports represented as menus, the door opening and hacking was supposed to be done by menus as well—but I decided to simplify aggressively in order to get something finished for the jam. That, and I had multiple sequences planned out too—some of the stuff in the prologue is a hint at what one of those would have contained. The epilogue was supposed to be linear, as that was the feeling I got from the song. Every sequence was supposed to have the final item mentioned in the ending show up in the first puzzle of the next one; this is probably less clear when there's only three.
But enough about how I wanted it turn out, and more about how it actually did. I guess it could've benefitted from being link-based, but I didn't want the headache of having to essentially build my own world model. The disjointedness was sort of deliberate? I was going for a sort of "reading a short story anthology from cover to cover" type feel than a singular cohesive narrative.
ETA: Linearity was probably also influenced by my decision to use ActorState objects to model where the PC is in the narrative.