Those omissions don't bother me, because I never had the original Subsistence version, only that single disc version that came with the 2007 PS2 box. The out of sync intro is a glaring issue, but it doesn't destroy the intro completely, so I'm kind of fine.
Could you elaborate on those "visual effects downgrade"?
What I'm worried the most is the audio department. Like I said, I know every second of those cutscenes and dialogues, so redubs will easily stick out to me. I'm aware of the redubs in MGS2, when Campbell is teaching Raiden the controls, awful. Are there any of those in MGS3?
I think every game should have full voice acting and plenty of cutscenes. I can't see any other ways to properly tell a story.