Possible Solutions - my 10 cents
Auctions - No, I don't like this idea. It might favour long-term players like me, but it's going to squeeze out new players and encourage RMT
Reverse Auctions - We actually have this system already. House prices start high and drop over time. I would agree the present system is deeply flawed though and starting prices are so low that it doesn't feel like the drop is significant. However, raise the starting price and you're back to excluding newer players (especially on a busy server) and encouraging RMT.
Lottery - Unfair and potentially frustrating. You could get the situation where a large, active FC could be waiting years to get a FC house, while Johnny-new-player comes along and gets a personal house first try.
Premium Housing Wards - No way! Please, stop trying to give a large and profitable company more cash so they can solve a problem entirely of their own making. They made this system, they are stubbornly sticking to it. In my opinion, it's their responsibility to make it work.
FC Apartments - Done right, this could be an attractive option. However a couple of small rooms, no workshop access or crossing plants plus a strict limit on utilities like bells, vendors, crafting stations isn't going to please anyone. So yes, this is a possible solution, but they'll have to come up with something far better than the personal apartments on offer right now.
FC Districts - I was going to say 'take my gil' until I read the bit about the number of active members. No. You're just going to get unscrupulous FC leaders spamming mass invites to keep their FC at the right size for their mansion. I saw something similar happen in WoW where more members used to mean more gold, it was an abusive mess and put a lot of people off joining guilds at all.
Instanced Housing - Honestly the only solution I could really get behind because everyone who wants a house could get one and we could do away with the demolition timer. It makes a lot of sense. I would leave the wards running for those people who love them and wouldn't like the change, though. Personally, I hardly ever see anyone else in my ward so it would make no difference to me. More houses sharing communal facilities like the MB would probably seem more social than what we have.
Fix Transfers - Seems fair, but it's not a solution really, just a more equitable way of spreading the misery.
Achievement based housing - This could be an interesting system for FCs and personal housing. I'd tie it to an instanced system with the achievements buying upgrades to your basic plot.