I agree with meteor2 regarding the differences of a big port vs small port regarding logistics, fuel tanks, etc…
But, in the end, all that matters is how the decision affects the game dynamics. For example, in WiF major ports can hold as many ships as the player wants, and minor ports have a limit. Independently of how well that mimics the reality, some ports in the game (Truk, Singapore, Gibraltar, Scapa Flow, Pearl Harbor…) have capital importance compared to the rest for this reason (partially, there are other factors like being between several sea areas).
Without that limitation, any port close to Pearl Harbor or Scapa Flow could substitute them… and that seems like a bad thing to me.
But it's just an opinion, as I haven't played the beta (sigh). I guess the optimal would be that during the development a few alternatives were tested to see what works best.