Currently houses cost the same for the same type of house, no matter if it's an FC or a individual that buys it.

This makes sense, a small house that's 4m for a FC, is still a small house for an individual.

Does this make everyone happy?

No, it doesn't. - In fact, it puts FC's bind to get housing faster for their members, before individuals buy them.

Should the small house only cost 1m for an individual?

No, the difference between a company and an individual buying the small homes is merely the involvement in a community.

Should there be instanced rooms that allow gardening/ect like in wards?

Yes, because the game shouldn't require everyone to be able to come up with millions of gil. - Keep in mind, they would be instanced and not persistent to visit like the wards.

In the end, SE kept housing consistent, and I can appreciate that, even with the grind it took for our large house.