Remade since the other was a bit buried, and wanted to post these apart...not so much thoughts as certain things I noticed. Some of these have been mentioned to a lesser extent, and most you probably know, but here they are regardless.
1) Brightness: even with the night vision (nice touch on the target boxes, btw), corridors remain almost pitch black until you step into them. This is with brightness turned up to full as well.
2) S'pht AI: In the second level (can't remember name any more...something about Bigger Guns), right at the end when the S'pht drop down, they bug out without fail every time and stop before they completely lower. This, obviously makes them very easy to pick off, as they just barely shoot the wall/ceiling every time. Not sure if anyone else saw this, but I did get it to repeat several times.
3) Pfhor movement: once again, not sure if it was something that messed up in my computer, but I had several Pfhor fighters freeze in their swing movement. Was kinda fun watching them float down the halls like that thought 
4) Hulks: No real complaint, awesome job here...but it doesn't take much to beat them with your fists, unfortunately. 
5) BOB. As per the ritual Vidmaster routine, these men did die. Quickly. The one note I did have though, the "They're everywhere" .wav sticks and can get very...very loud when it sounds like a broken record.
6) I love the addition of extra movement when the hulk decides to show you his throwing arm (had it popped into godmode to check out some of the animations up close, and that was a very special bonus). I spent a good 20 minutes getting one of those to hit a Pfhor...wish I knew how to record that tho. It was a classic moment.
7) Another S'pht note, right where you get the assault rifle, there is a S'pht in that area that almost constantly gets stuck in the alcove almost to the ceiling. Not much trouble, but I have seen him get stuck inside the wall...letting him shoot out, but not get shot. Might be related to the problem I mentioned before.
That's all I really could think of to ramble on for now Spent a good long while running it through the ringer (this is special...I've now done testing/beta testing on the first Marathon 2 times...both generations. Ooo la la), so hopefully some of this helps. Definately can't wait to see the finished product, keep up the good work! 
