Art: There isn't much of it, and designwise, everything is monotonous black. Not much to be said here, but I imagine you know that.
Writing: I think you're someone who can write well in the important ways. You've hit the right balance between straightforward description and vibes. However, a lot more time and care was needed, especially for the interior spread. The writing on the exterior is reasonable except for some little technical things (it's/its, unnecessary repetition of certain words, etc.). Interior is a bit more stream-of-consciousness and thus disjointed. It would have been worth it to make notes and plan structure first before writing any of the final text. E.g. the first paragraph on the left panel of the interior addresses about three different topics that should have been separate paragraphs.
Game Design: I think the narrative structure of a pick-up-and-deliver quest with a dangerous item works well for Mothership, and I like the way you designed the constraints and risks of handling the object. Everything else is a little too roughly sketched out. Like the writing, it could have used more careful planning before doing. Not sure why an NPC captain is given for the Promethean when it says "unknown" captain in the header and that one of the PCs will be the captain elsewhere in the module. Also, he has the same name as the Eagle's captain... are they meant to be related?
Theme: It's there, but only as a single paragraph in the intro that has no bearing on the plot. You did sprinkle some mythical names in elsewhere, but in a kind of piecemeal way.
Layout: It's a bit messy overall. Running important text across the fold on the interior spread is questionable in that creasing and ink wear might make it hard to read. The texturing and tiny size of the malfunction table make it hard to read, while the ship names and stats are way bigger than they need to be.
Utility: There's a lot that's been left up to the Warden. The text implies that we're doing an exploration scene at the base, but there's no map. The encounter with the Eagle Gallant is important, as it's the conclusion, but the ways that can play out are kind of spread throughout various sections. Maybe a flowchart would be appropriate for handling that.
Favorability: Despite my various criticisms, I like what you have at the heart of this. The execution is lacking but I'm giving you high marks for favorability because with proper planning and a lot of rework, the adventure concept is a really good one. I like that you have a Bad Thing that doesn't just turn everyone into monsters and a clear setup that leads into an endgame where things could go a number of different ways and allows for player agency. And a good mix of exploration, problem-solving, and combat.