I mentioned something similar earlier in this thread, allow me to amend and expand on the notion a bit.
Rather than a guild size bonus, or a ship size bonus, institute a "maintenance fee" or "tax" based on the ship type.
These numbers are for example purposes only. I assume that turbine will set these amounts based on what they determine to be their own best interests if this system or one like it is adopted.
Windspyre Sparrow: None
Stormglory Bolt: 44 renown/day
Windspyre Falcon: 2000 renown/day
Stormglory Tempest: 2250 renown/day
Windspyre Gryphon: 20000 renown/day
Stormglory Typhoon: 20000 renown/day
Now, this might be seen to unfairly favor large guilds based on the same (flawed, IMO) logic that declares decay based on guild level irrespective of number of players unfairly favors large guilds. So to counter that we give each amenity renown "upkeep" an number of uses between "upkeep payments". From a lore standpoint, these are seen as being available to you because you are well-known as a protector of Stormreach (and also the rest of Ebberon and the forgettable realms), but if you're seen to rely overmuch on the help of others (shrine-makers, crew members) you'll lose a bit of that prestige. Or you're flush with cash and can bribe your way to whatever you want (Astral Shard prices)
Disclaimer, again:
These numbers are for example purposes only. I assume that turbine will set these amounts based on what they determine to be their own best interests if this system or one like it is adopted.
All gold seal amenities: No renown upkeep
Pawlo Mapmaker (L1 Navigator): 50 renown/100 uses (you're helping him make maps by exploring the areas)
QoL amenities (bank, mailbox, etc): 75 renown/100 uses
Lesser Resist Shrines: 100 renown/100 uses
Non-navigator Crewmembers: 100 renown/100 uses
Artleblat (L2 Navigator): 250 renown/100 uses
Trap Device, Stone of Change: 300 renown/100 uses
Standard Resist Shrines: 500 renown/100 uses
Twelve Planescaller: 700 renown/100 uses
Shroud Altars, Epic Altar: 750 renown/100 uses
Greater Resist Shrines: 1000 renown/100 uses
Xathrizopkrsis (L3 Navigator): 500 renown/100 uses +50% increase in renown upkeep from other crew except House J healer (ZOMG they fly around with a Mindflayer, What's up with that?! Creeps me the math out!)
New crew member, Gold Seal only: Orevale and Walbar Shipwright -- These master airship mechanics can be hired to help maintain your guild's airship, but be warned, they don't work cheaply! (Price: 400 Astral Shards, standard gold-seal amenity duration)
Then we uncouple all of the ships and all of the amenities from guild level, and just let guilds pick and choose what they want. If they want a big ship with all of the buffs and amenities, they have to earn more renown to keep it than a more humble guild that gets by with a small ship and a select few amenities. And anyone can throw money at Turbine to get whatever they want.
This would hurt small guilds even more than the current system. That would only accomplish completely destroying small guilds and creating super ones. What small guild can afford to pay renown daily for every ship buff?
Again i say, the ship buffs are the issue, why not remove them.