Unfortunate, but not surprising. We have decades of precedent of letting people do whatever they want, even if it is against the established design guidelines. Gate just did what several others have in prior months, years and decades.
Unfortunately, the reality of Jax's situation can be boiled down to this:
If you can't get a gas station design right, what does that mean for establishing a walkable Brooklyn or downtown in the future? Placing my heart aside, my logical side would say you can't blame Jax's suburbanites for not wanting their tax dollars wasted in downtown. Hundreds of millions spent over the last five decades of revitalization and today's environment is what you've gotten as a result. Thus, when a Landing redevelopment plan or Shipyards proposal (both of which call for huge public subsidies) goes up in smoke, I'm one of the urban advocates who still sleeps well at night.
I'll stand by my statement in another thread that downtown's vibrancy (or lack of it) is less about the financial and more about getting public policy right and sticking to it.