SE is aware of rank related issues though it's been almost 2 years since they said they were considering what changes to make and implement.
https://na.finalfantasyxiv.com/lodes...b1046155e63703
Hopefully it's a topic that YoshiP will be revisiting in the Live Letter this weekend.
They did stress that it's up to the FC Master to use caution when granting ranks promotion/demotion privileges (or any other rank privileges, to be honest).
As for some of your other comments/ideas:
That isn't a problem with SE and the FC system design. SE rightly doesn't want to dictate what activities a FC can do. If your FC feels like no more than a glorified chat room, that's a problem with the FC leadership. It's up to the officers and members of a FC to organize activities for the FC to do together. There are a lot of FCs that will actively farm content together and hold other events because their officers and members put in the effort.Problem: FC's are glorified chatrooms with attached buffs and a pretty house (sometimes)
RE: company credits - very active FCs will inevitably end up with a surplus of these just as very active players end up with a surplus of gil they'll never spend. MMOs can't be balanced around the most active players that earn more because that leads to frustration among new/infrequent players when they can't get the items they need/want due to high cost.
Still, there are some things SE could do. Top of the list to me would be add the grade 3 FC buffs to the GC QMs for purchase with credits so even FCs without a house will have access to them.
Second would be to make Company Credits the currency for purchase of a FC house instead of gil (that would put a big dent into shell FCs used solely for house flipping and/or workshop profiteering). Small but active FCs would still be able to earn enough credits to get a house though it would take some weeks instead of a brand new FC being eligible to purchase a house within a few hours of creation.
Third would be add more items to the GC QM and Resident Caretaker that can be sold on the MB for gil that FCs could use to fund their activities/events. The dozen or so items that can currently be purchased and sold on the MB aren't worth much because all FCs are selling the same thing.
One thing that SE should do is restructure the amount of Company Credits generated by certain activities (especially activities that are done solo). Crafting and Expert Deliveries seem to generate a very high amount compared to other activity and that puts FCs that focus on other content at a disadvantage.
RE:Fellowships - there's nothing stopping a FC from creating a Fellowship. It's not something that needs to be added by default when not every FC will want one and they are simple to set up if a FC does want one.
RE: all the new ranks without perks - my guess is that was intentional so FCs wouldn't feel pressured into gaining all the new ranks as fast as possible. Now SE can add the perks at a later date and the more active FCs will automatically gain them. It would have been pointless for SE to add the new ranks without some plan for them. Prestige isn't gained from getting something that has no purpose - it's more likely to make people look like fools for wasting their time.
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It would be nice if you gave a bit more information about Lost Ark's system. Saying "weeklies, research" doesn't do much to describe what those are and what value they offer.
I remember WoW's guild level and perk system, and how it ended up a problem in the long run. While a formal structure can seem like a good thing on the surface, FCs should be free to create their own meaning and identity rather than have the game dictate it or offer a reward system that ends up abused by FC leadership.