The Tower would still have to be loaded up anyway, so the only time you'd be saving is the time spent navigating through the Director to press "Set Destination->Tower->Launch". Also, there are rumors that the Reef is a hub area/social space too, so that once you reach endgame you may actually want to go to the Reef before you go to the Tower to check in on stuff.
EDIT: As a personal note, there have been far worse systems of transfer in games. For example, transferring all of my Pokémon from Black 2 to Y took me 4 hours. If you manage your gear right, it will take you 10 minutes tops to transfer gear from one character to another.
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Time saving as it currently stands [i]if[/i] you assume that had we been given the option of loading straight into the tower that we would also see our spaceship animation. What if from logging in directly, you completely bypassed that animation as well as the obvious selection process? That would be a substantial time saver.