Ya know, prior to all the complaining about the Mission Objectives not beeping anymore, I didn't even realise that they DID beep, as I've had the sound turned low on the game cuz of all the humming SS and whistling forcefields.
Personally, I don't have any problems with I3 the way it was released, as it has not hampered my playing of the game. Some things are different, yes, but I guess that adapting to changes that may be detrimental will just keep me on my toes.
Heck, just consider it a plot complication, similar to a enemy discovering a weakness of yours and exploting it. Even Superman had his kryptonite.