Okay, here is a list of what was reported thus far in this thread:
1)Ugly backgrounds/planets
2)In swimming with the sharks, the Shivan corvette does not die if not sufficiently pounded
3)The Sai and the Lonewolf have sex
4)Reported misses by the Narylathotep(damn I suck at names) in the mission with angry civies
5)Reported misses by the Narylathotep in the mission where it undocks the Arcadia and supposedly kills the Sobek.
I will go through them as I get to those respective missions.
But first, addressing 1). I've modified the mod.ini to run with 3.6.12, and I must say the backgrounds and planets look lovely. So really, I don't see a problem there.
Now for the missions, I've only been through the first. I'm a lot slower, but more meticulous. Here is what I found:
-The loading bar is very very fugly, it actually looks horrible. wouldn't mind doing something about the background image when loading.
-CB ani's would be really really nice
-At one point in the briefing, ore carriers are mentioned, and a wing of freighters is shown on the tactical display. However, when you click on it, you are shown a TC-TRI. I think you should see a Triton.
-Let the cargo container that's supposed to be stolen by the Blackbeard loose a little life, it looks odd when it has 100% life and the freighter just blew up next to it.
-THIS MAY BE MEDIAVPS RELATED: When you look at Poseidon 7 from the upper-back side, the Poseidon is lighted by its own engines, however those engines do not light the container as well, which looks hella ugly. Pic included for demonstrative purposes.

Sorry for the red screen, couldn't get it otherwise
-THIS MAY ALSO BE MEDIAVPS RELATED: When I hit pause, or exit, in Retail or the old vp's, I usually got the Paused thingy, over the frozen screen from where I was at in the mission. However, nowadays, instead of that, I see the Paused thingy with either:
a)a single colored background
b)an image from earlier in the mission
c)a heavily distorted version of my current image
-In my second playthrough, the Blackbeard got killed by those 3 Tritons, before I even got to 10000 m, which was... very weird.
That's all I could find for M1.
Oh, and for the May be MediaVP's related thingies, don't kill me if they really are related and I posted in the wrong thread. I DO NOT KNOW if they are related.