Not that things would have to be done this way, but here would be my implementation for the specific issues you raised:
- Guild ships - The guild leader is the guild owner. The ship and all amenities remain the property of the guild leader. Others who contributed lose nothing as long as they don't leave the guild. Or phrased differently, they lose exactly the same amount as they would lose if the guild leader disbanded the guild, which is within their power to do at any time regardless of how much anyone else has invested in the airship or amenities.
- Astral shards - Adding the Server A amount to the Server B amount seems like simple arithmetic.
- Character slot maximums - The prior server mergers are before my time. But from my discussions with people who went through prior server merges, in the past character slots were simply added together. If you had 45 characters and slots on Server A and 45 characters and slots on Server B you'd have 90 characters and slots on the merged server. So there was never any loss of character slots or any need to make a purchase before playing your characters.
- No one is being merged onto the same server they left. They
might be merged into a server which is the amalgamation of their old server and their new server. I'm not sure I see a problem here. They are not losing anything they had on their new server, they are simply gaining the population of their old server. The same thing would happen if everyone from their old server decided to pay for a transfer to their new server, just as they obviously did.