Let me see if i can explain more clearly.
Let's say i have a level 8 port and my opponent has a level 3 port. Under the new system we get the same resources from war because rewards go straight into storage and bypass the port. However, lets say upgrading the port those five additional levels gave me 250 additional experience points. If my opponent has the same experience points as i do then they were able to use them for offensive or defensive capabilities where i wasted them (and my resources) on upgrading a useless port. I am at a competitive disadvantage.
At the end of the day, this is not really an issue for me. Its mostly academic... Although I'm sure people spent gold in upgrading the port either directly or through the use of shields to acquire the necessary resources. The issues that people really have are that they needlessly wasted time, money, and resources upgrading something that later turned out to be useless and probably more importantly, that FTX made this change for only one reason that players can fathom, to take away the ability to shield resources from a raid thus requiring more use of shields/ gold to save for upgrades...