I can't speak for all servers, but currently Sargatanas is pretty much chocka block (full). My FC are saving patiently for a medium (we have about 10 active members, everyone works full time, it's slow going :P) but currently on Sargatanas there are 0 available. When they add that 1 single whole new ward to each zone (which I think totals 14 new medium homes) we're still a long way off having the money for a house at full price, so we'll be waiting on it dropping again, whilst continuing to save.
My point: couldn't we have a system whereby FCs which are no longer using their homes, or the FC is even active, can sell the plots to another FC? To prevent abuse of this just make it so you can't sell it for more than the price of the house would ever drop to (so around 15 million or so I think for mediums).
It seems at the moment there's a lot of abandoned or inactive FC houses not being used, and people probably don't want to lose out on all that gil they dumped into it, this would at least ease the pain of that and maybe help other FCs such as mine.
Also, one thought we had was to just buy a small and continue to save for a medium, but again, waste of gil, it'd be better if we could sell on the plot, even if it's at a loss.
One more thing, I know it doesn't address the issue when FC leaders are just... gone, but we're still waiting on that fix from SE, nothing we can do about that.
I can't see any loopholes in my idea, but feel free to nitpick at it, that's why I'm posting it here \o/