Fr5s are almost never used these days. Impact on the faction is minuscule anyways - unofficial factions get player requests processed the same way Official factions do. Your power over own indies is very small because you need to cater to them in the first place so they might join you.
Impact on story is gone - official factions are ignored and buddies of Reeves know more and get more done that Official Factions themselves. Ofs don't even have control over their own reps often these days. Perks get denied well, even when you put in hundreds of hours of work you get just ignored.
My point is you don't need to be official to play the game not at all. I don't think there needs to be a system change because official factions don't really matter in the grand scheme of things. And that's not a necessarily bad thing. You go after perks that are nice to have but not vital. Forum, own ID, extra lines, approving tech for others - those are nice things to have but not vital by any means. If you fail officialdom it's not the end of the world, all factions don't need to have an OF really.
Ageira has given up, to keep up the 3 days you need one thing and one thing only - a single interested person in the faction in leadership. That's it, nothing else. The benefits of being an OF weren't worth it for them to play the game.
I run Mollys and Core Force. 0 Ambition, 0 requirements, work only when it's fun and it works perfectly fine. It never occurred to us that we'd need to go for officialdom. Or in the case of Mollys even be on tracker. Factions like FLG need officialdom because the indie ID is outdated by many years without staff bothering to update it.
Some lawful Navy factions I feel need to have their sub forum first and foremost because of overload of threads, be able to do blanket bounties for indies, be in the OF list so people know they exist to keep the region alive - keeping up activity is worth it there and we make sure we log the necessary time to take it.
In the case of Ageira? Honestly, I am not surprised they have given up on it - not being official will have close to zero impact on them. Trading companies without a mining bonus in general I don't feel like have any incentive to be official besides "because we can".