There are several things SE needs or could do to fix up the housing system. Not just having a abandoned housing system that works on a long timer. It's going to take a bit more than that to get the loud ones to pipe down.
SE just needs to give everyone customizeable Inn room. I would bet the majority of those complaining would be content if they could have something to customize and call their own. Let players get it early on with maybe something tied to the story as you progress. Similar to how retainers were given to us. Those Inn rooms could have a smaller item allotment of like 25 or so since it is a free item. Then let the next step up be the personal rooms for being apart of a FC. Then after that a personal house or a FC building.
Then for the actually ward housing plots. Those are things that need to stay limited. Having a big and awesome house should be a privilege to show off and not a right. Each server already has 1440 houses between the 3 ARR city-states. Then if some sort of Ishgard housing area if not something around the Sharlayan area since dragons and being assholes. (Oh hey look our new hou- *System Notice: Your house has been burned down by a Dragon attack*...) Anyways, with 4 housing areas that would bring us up to 1920 plots. That's already a pretty sizeable number before you add the potential 4th area.
But the real issue is the items tied to the housing plots. One being the Chocobo stables for many players that I've seen complain about housing. They want to dye their Chocobo or stable them and feed our favorite yellow fluff balls food. Why not let some of the open world stables accommodate this? For instance there is a big stable in Bentbranch in Central Shroud. There is even a series of quest you go through around those early levels. Why not after completing those quest have them open up their stables to be used to the same way the current housing stables are?
Then for gardening...Well I got nothing since it's sorta dead right now. Archeage style open world planting and harvesting was fun but I don't see it fitting with this game. Perhaps maybe their idea of public gardening plots?
All in all it's going to take a few changes to several portions of the current system to better help accommodate its popularity.