The new start system is a bit more realistic than the old one, however it's become much easier to defend (especially with the retreat system) and harder to hit (a good thing, I think). But, really, unless a mass bomber mission forms for the sake of realism or a fight, nobody bothers to attack them in force. My reason for not doing so is knowing that the second that HQ or troop factory drops, a big rush of goons will have it back up in a couple minutes.
Removing the ability to manually supply factory, city, and HQ objects would greatly increase the desire to attack them, and equally require player power to defend them. It takes a keen bomber pilot to scratch a new factory when undefended, much less when it is, so you don't lose much to the average-Joe scoremonkey at 30k, but a fight can easily start over a strong push at the factories when they're actually at stake.
Also, I'm for returning to the 4-section HQ system.