I'm sure this has been suggested a million times but in the off chance it hasn't, what if instanced housing was created for FCs only. The whole "neighborhood" idea is nice but i feel like it's not needed when you have an established community like an FC. The size of the house could correspond either to the size of the FC or the FC could spend gil and/or other resources to make it larger over time. The latter also being good for smaller FCs who want a large plot with apartments for their members. This could also sort of fix the shell FC issue as if you want to create a shell FC to create you're own instanced house it's not effecting the community at all. The FCs that already have a house would be given (X) amount of time to relinquish their plot for a full refund (as well as members who purchased a room) so they could create their new instanced house.
I'm sure there will be server issues to deal with but it sounds like they might have to expand their server capabilities anyway if they are going to tackle the housing issue as a whole. Plus they might be half way there with the new island sanctuaries. This would also keep Yoshi's original concept of a neighborhood as all current housing would be personal plots. I would think this would free up a significant amount of plots in the short term while SE expands their capability to create more wards or whatever their plan is to increase supply long term.