My impressions of level two:
I played TC and thought it was fun. Scratch starting is touch and go until you get the Zeus. I liked the puzzle in the little machine room with the red herring bobs and I liked the Pfhor fighters loafing, catching some z's, smoking, in the cool fusion chamber area. I wonder what the punishment for loafing on duty is?
Re the two switch 2x charger. Later in the scenario I went back there but the switches no longer opened the door. Does it only work a set number of times or is there something somewhere that disables it?
Also, you have all these secret platforms where Bob corpses are. Is this simply there to crush live Bobs for scenery purposes?
I don't know about the secret crusher (?) platforms, but in this type of action I would expect to see lots o bodies lying around. The Pfhor are not friendly folks.
More variety in texturing, as I'm sure you know, would improve the level.
I got the impression that most of the customer/visitor traffic would be by transporter so what I was in were basically service areas/routes which probably wouldn't have a lot of interior design attention: I've never been struck by a lack of variety in any of the Marathon games I've played. I can see the lack of variety in PiD (I've not played but I've watched videos), but that is an extreme case and I don't think your map is anything like that. I really liked the final room - if I owned the tower, I'd make it my personal lounge.
I went and looked at the other weapons and they're OK except I thought the toaster was way too powerful. And while the napalm grenades (?) are interesting and fun, there's just something elemental about the wall of flame of the ordinary toaster.
I'm actually pleased with the new gun and monster physics, but I know not everyone is going to like it.
Your map is a different environment. It's possible that planetside weapon variants might have unforeseen drawbacks in space and wouldn't be used there but would still be common on the ground. I think your changes are justifiable and it isn't really all that different. I like it and it doesn't jar with the rest of my concept of the Marathon universe.
I don't understand about nonlinearity. I don't expect the terminals to be chronological, after all I'm snooping, and if you're talking about the building, any large building is a labyrinth once you get out o the public areas.
I noticed that polygons 288, 646-649 and polygons 1000 - 1007 (though I don't remember seeing 1001 & 1004) don't have any sound. I wasn't looking for this but I noticed the silence and used F10 to see the number. I know nothing about mapmaking so just referencing the polygon number may not be sufficient?
This is what a Marathon "remake" should be: a parallel story planetside. Depending upon the size of the colony, there could be several stories there. You already have a second story going. If as you say "the player character is searching for someone" I would hope that to be Shotgun Sally who sounds like a capable person. Obviously not your run of the mill technician. Reminds me of a cook on the USS Missouri.