The capacity is 3 million not 5 million! It has said it on their own website since the very beginning. The 5 million figure is one they say they can expand to by adding a pier to the north toward the cargo terminal (who'll pay for it?!).
The factors mentioned above are all genuinely annoying things for users, but the fact that this terminal was designed for 3 million, a number they may hit this year, is the biggest scandal of the lot.