Whilst I agree with you about the personality differences between The Major in the original film, and the entirety of the rest of the franchise, my personal feeling is that they should not be regarded as different timelines. The difference could be down as much to the different English voice actresses and animators as anything else. I wish I could understand Japanese so that I could judge whether this is the case in the original soundtracks.
I have heard other people talk about this, but I can see nothing in the ARC of SAC that would conflict with the original film happening later in the same timeline, and it is quite clear that what happens in the original film is necessary for the two following films, inclusing SSS, which most people think is in the SAC line. I don't want to go into details, because some people here may not have watched them, and I would not wish to colour their experience (except to say you must watch them, especially if you think animation is just for kids - careful of the 1st Gig episode "Jungle Cruise" though)
And I believe that if you watch the retelling of "The Laughing Man", and "The Individual Eleven", there has been some re-working of the SAC animation (new/different scenes) and some re-voicing of the characters (I was quite shocked at the differences in the bits I have seen). Both I and my daughter think that these later re-packages are significantly worse than the original. These again change the feel of the series.
One thing I always find strange, and that is the way anime series are often re-cut to create a film, but the re-cutting, or re-imagination whatever you want to call it, results in a completely different telling of what looks like the same story. This started a long time ago, and the earliest I remember noticing it was Macross the series, and "Macross - Do You Remember Love". Wherever I can, I try to watch the original series in preference to the films, but that is entirely dependent on what is dubbed into English. This is why I sometimes resort to fansubs on P2P sites, as I don't speak Japanese (did I say that already?)