Okay, a lot to get off my chest, but here goes my thought work on a remake (IE, mostly faithful, but adding sufficient plot filler and enrichment) :bluelander:
So instead of Miria being sent off on the space crusade alone, she's part of an elite cybernetic enhanced team called the Guardians (For namesake :bluelander:) Who are deployed after the whatever-we-call-the-coalition-space-government tries to stop Naju hurtling towards them, then hopes that the small, agile fighter forms can find a way into Naju to discover a way to stop it, or destroy it. This could give Miria a group of "Peers" to interact with, and allow emotion and personality. I'm suggesting just a group of four, with each Guardian having an unique specialty, so they don't all follow Miria through basic foot sloggin around Naju, so we retain your freelancing exploration. Of course, some milestones in game progression could spark Objectives that bring some of you together, like seeking out another transmission in the ruins of Naju, or stemming a surge of invaders from your "home base".
More on the Guardians. I figure there's a requirement for team mechanic/engineer, maybe another female. Another could be something like the team scout, recon runner to map out the way for you in some areas. Then maybe one would be a type of captain, the guy in charge. Now, I don't want a sci-fi romance novel, but Miria could have feelings for someone like the captain, who you think dies earlier entering Naju, so we can see some passion and sadness from Miria. But not to make her seem weak, or overly emotional. I still think of her as a stoic, Samus Aran style warrior (Samus as in, Not Metroid Other M).
Now, on plot thought, I've considered a reoccuring or at least, often present villain, a nemisis you learn to hate and wanna kill. Maybe a betrayer of Naju who has something to do with the invading aliens takin' over. Maybe even created them!
Okay, that's my best on TGL remake/sequel. Hope this is either inspiring, or thought invoking. Hope none of this sounds to generic!