So I can understand people thinking these are unneeded, I too dislike them. Took a moment to think about all the transitions and came to a thought as to why they are put in.
They are there for story transition. So your on a quest, you run back to your ship and suddenly get a cut scene when you enter the hanger, or spaceport, or elevator.
Should Bioware have put in a better way or found a better way to do this? Yes! But it is what it is, until they do you will have to deal with the transition areas and no instant access port to ship.
Just my thought on it. Disagree if you want .