In my experience nothing keeps players in a game more than making friends. As of now, guilds give advice and some help a bit new players financially, but once a player becomes established guilds lose most of the relevance. Nation bonuses are great, but maybe we need to keep in mind that there are a lot more nations than ports. I think that making guilds more relevant could make it more fun for all and help the game as well. Some ideas:
Guild Wars: War between 2 guilds declared officially should be treated differently than plunder. Maybe only a set amount per guild as loss/win instead of individual wins/losses, keeping in mind the guild strength. For example: a guild with 20 small players should make more money if they win against a guild that is stronger. Strength could depend on type of ships, number of fleets, fame/influence. Player activity should have the stronger impact on the war, so maybe require less turns per attack during a war?
Guild Inventory: Members would be responsible of building common inventory. Something like a fix number of ships at the time that can be gifted to members, voodoo cards, gold, materials, or all of the above. Obviously the milking rule should be in effect - what I have in mind is help for the newer member, or an older member in big need, not 20 members building inventory for 1 player. If common inventory is hard to implement, maybe the ability to send voodoo cards or ships/more cash to guildmates, although I think common inventory is better. Ships could be on "loan only" with guild being able to recall the ships at any time - or fleets instead of ships. Guild creator should have the option to allow members different levels of power (like we have now): receive for all, then loan only, send loan, buy from market, sell. For gold or voodoo cards should be send instead of loan.
Guild members activity: A daily bonus for the guild based on number of members that logged in that day and hours played - it doesn't have to be big, just something else to give a guild common purpose.
Guild Port: Something like nation port, influence requirement and some kind of bonus.
Hopefully other players have more/better ideas how to make the guilds more relevant, but I do believe an increase in relevance would be better for all long time.