A few things I've noticed thus-far:
-For some reason, my hud resolution is down... meaning that hud elements are back to the relative size they were back in retail. I'm not sure if this was intentional or not.
-More of a suggestion... for "The Place of the Chariots", the asteroid field is supposed to be a dense one, but the existing field looks rather sparse. You may want to consider importing the pre-formed asteroid fields used in SaH... perhaps narrow the size of the auto-generated field and then fill the surrounding space with these.
-During "Lion at the Door", I've noticed that one of the CB-Anims could use a face-lift. The one showing the Carthage and Dashor jumping out, has the Dashor as the pre-Hi-Poly model. Something to look into for later releases.
-During the briefing for "Mystery of the Trinity", the briefing icon for "unknown", which is supposed to look like a bit of nebula, looks like an Orion.
I haven't gotten to the "Trinity" mission itself yet. I may come up with more later.