As an owner and builder of structures: A token cost to maintain is fine. It should be low but at least required. If it is higher than 5 blocks per hour, then the cost for service modules should be lowered by a relative amount based on how many service modules can be fitted.
Indexing won't help unless it is a simply +1 for X amount of additional structures present because unless the base cost is very high, an indexed number won't make a significant impact. Also, such an indexing scheme can be used to grief the smaller players whose isk supply or access to fuel is not as great.
If you want to get rid of the glut, CCP would be better off limiting the number of structures per system - especially in High Sec.
In terms of the consequences when fuel runs out: Loss of basic functions makes sense: no teathering, obviously any service modules will be offlined because there is no fuel anyways, defensive systems go offline, and invulnerability drops. The structure can still be docked in and offices accessed. There should still be a reinforce period after the shields go down giving the owner time to try and save the structure by adding fuel before the reinforce comes out.
One additional caveat should be added: when you get into structure, between 99% and 50%, the structure can be claimed by the corporation having delivered the most DPS. Fuel can be added and the repair cycle carries out - barring the structure continuing being shot.
The restriction on refitting weapons should be adjusted so that you can drag a different weapon over to replace one currently mounted (service modules and rigs should still be locked during reinforce periods but you should be able to swap out modules, add ammo, fuel, and more fighters) unless there is a weapons timer on the structure.
After all, these are not POSes, but different kind of structure. Parity in base functions but not parity in limitations: these are not improved POSes, but something new.