As we know, Vidiot over on the SHTV forums had done some work on the 2004 trilogy ans has given some insight in the past as to how things were done. Recently, he's mentioned a few things which make perfect sense: That it was a bit rushed, understaffed for the scope of the project and continually tweaked and re-tweaked. This would account for many of the issue we have bemoaned for years and years.
But he did say that both the claims of no negatives existing, or that they were conformed to the SE were pretty much bogus.
Nice to have some confirmation for a change isn't it? ;)