As you said, you don't see the big picture. Those cells were probably causing other departure gates to get jammed and bottlenecked. Keep in mind you have departures from PHL but also EWR, JFK, LGA, TEB, HPN, MMU, all squeezing into the same gates while at the same time arrivals for all those airports too. You might say well why can't we just go that way instead? Well because arrival streams to a dozen other airports are over there. In the NE corridor between D.C. and BOS there's pretty much an arrival or departure route everywhere. No amount of modernization will change that. It might straighten out a couple routes, but it's not going to allow departures and arrivals to play chicken with each other.