To clear up your points: the missed payment in question was not for a single starship but for the structure that designates control over a system. Simplified, the mechanics are such that so long as this structure exists taking the system is a difficult affair that favors the defender (structures have huge amounts of hp and then a invulnerability timer that gives defenders hours to realize they are being attacked and mount a retaliation). However, fail to put the resources into it and the time consuming step of removing sovereignty from a system is removed and the battle is more equal for both parties.
The way EvE is structured lends itself to shifts in the balance of power. Just because one faction is on top today doesn't mean they will hold their position indefinitely. The victors here, for example, come from much humbler roots and, when they entered the game, played a crucial part is annihilating the current ruling power.
All thanks for the replies. Makes more sense, but I would have put it in as "this defense system needs X amounts of this rare fuel Y each Z" (or, maybe, bring a statistical aspect into it: "the Foo in your bar are wearing out faster than usual. Please make sure you have spare parts"), not as "yes, you have a zillion extremely powerful guns, but if you don't pay rent in time, we, will take your guns away from you.". This, to me, makes this universe feel like some toy system with some all-powerful entity who really is in control (a bit like Q, but less disinterested).
Also, what would an all-powerful entity need that money for? It would have to be some accountant-deity to enjoy such regular payments. Or was that apparent glitch that showed the bill as paid to some part of the fun?
The way EvE is structured lends itself to shifts in the balance of power. Just because one faction is on top today doesn't mean they will hold their position indefinitely. The victors here, for example, come from much humbler roots and, when they entered the game, played a crucial part is annihilating the current ruling power.