I also played through the entirety of MM (well, actually only story- and sidemissions, didn't get all the hearts). The only thing that I noticed was that the cow in the alien cutscene didn't have a nosering, the cows in the barn do. Not sure if this is intentional or the same way as the original, it'd be a bit weird consistency-wise if it is but I guess its just a minor detail.
Then there is of course the corrupted screen issue from the bombers notebook, has there been any research done about this yet? Even if its just pointers to the relevant code sections or speculations about what the cause for the issue could be.