Ok, this suggestion is intended as a kind of interim solution to small orgs not being able to get player cities.
APF could include a small instance-on-demand PF that works similar to a player city's alien raids. The basic idea would be a mini-apf that you can only assault if you load up the base's defenses (with CRU of course), and then you get warped to the playfield with a boss at the end. Kill the boss and get access to an alien ship, same like the normal city. Of course the shields come with maybe a 2 hour lockdown (for lowering again, re-raising should stay at 1 hour because that's more a hassle than anything else) as opposed to 1 hour.
To join the task force that allows you entry to the base, your org must pay a monthly fee (say, for fuel for your ship that takes you to APF), and you could even get minimal city benefits (e.g. Org pres selects 3 advantages out of the list when signing up - but not all so that it doesn't become more than what a small city could reasonably fit) and a player shop.
Now of course it would not be as good as a city, but the key thing is that paying customers who aren't fortunate enough to purchase a 5 billion cred city from one of the real estate agents will still get access to an integral part of alien invasion content that they paid for without in-game restrictions. There would be no lack of real estate concerns from such a place either. Or heck, tie subscription to an individual account, rather than an org, so you don't have to worry about org ranks and remove org advantages.
In short, make "content-on-demand" actually available on demand.
Edit:
Someone pointed out that people making farm orgs could easily circumvent the lockdown to hop orgs in order to farm 24/7. Fair point. To prevent this, there should be a cooldown nano in the individual toon's NCU to prevent him from coming back for 2 hours. That way, only a well built, decent toon of the right level should be able to trigger and access the content, and only once every 2 hours.