Art: Full marks. The illustrations and map are perfect. The graphic design and typography are a bit boring in comparison, but it's functional and easy to read.
Writing: Good on a technical level and does what it sets out to do, which is to provide an excuse for your mechanical creativity. That's fine as it goes, in that the writing isn't the selling point here. The setup of an alien artifact that turned everyone into monsters is a Mothership cliché, and you've hybridized that with a fairly off-the-shelf interpretation of Cthulhu mythos. Professor Warner hasn't been given any personality.
Game Design: Stacking the dice is a clever visual gimmick and timing device, as is using it as a way to balance out the degree of luck. However, having to place them upside down is fiddly and I expect some groups will get it wrong. Since you're using tables anyway for the exploration phase, why not assign the worse/harder outcomes to the low numbers and make high ones better for the players, so you can just stack them as you rolled them without worrying about reverse sides? The scenario itself doesn't provide players a lot of options to tell the story they want. Either they're going to visit every room one by one and then deal with the obelisk, or they're not going to have a game. The keycard ending is bound to be anticlimactic and, for players not inclined to be good sports and just go with the flow, there's going to be a powerful desire to blow up the power generator and put an end to things as soon as they see what's going on.
Theme: Full marks. Cthulhu mythos is such a natural fit for Mothership that I'm surprised more people didn't use that as their mythology.
Layout: Full marks. All the information is where I'd expect it to be.
Utility: Full marks. Everything is here that you need to run the module as intended.
Favorability: Personally, I'm not big on scenarios where the story is largely being driven by dice rather than player decisions. There isn't much to do here except pick a random door, have stuff happen at you, and repeat until you get to the end. Players who have other desires are going to end up derailing the intended flow (e.g. trying to destroy the generator immediately as mentioned above).