They should have never shoved personal housing in with FC housing. They were supposed to be separate and Square Enix went back on their word.

I would suggest having neighborhoods for FC's only, and other neighborhoods for single players. This might leave the solo neighborhoods empty, but people barely use them now. They could also make instanced houses with a yard. Also, have the option of having something like the inn rooms for players who only care about decorating the interior.

For stuff like chocobo's, make training and such available from the chocobo trainers in bentbranch. Pay a fee and they board your chocobo (like how you board horses in rl). That will give people the ability to dye and train their chocobos without having to own a home.

For gardening, they could make indoor pots/planters that you could grow stuff in. That way it is both decorative and functional.

Tada, most problems would be solved.