I have a suggestion that might help on other areas also. It refines the OP's current summary just a little bit.
I have seen many posts about various ideas to bring people back to the older parts of the game. SE put a lot of effort, in the past, into developing the various story lines and expansions, so incorperate them into the Mog House expansion process.
Make the Mog House expanions only available after completing each of the various story lines. Each story line has a different expansion associated with it.
For example: Attain Rank 10 in Sandoria, and the next time you zone into your MH, your Mog tells you that you are eligable to expand a specific portion of your Mog House. (per the guidelines/requirement mentioned in the OP's summary. Materials, gil, a misc quest, minimum reputation in that area, etc.)
Each Rank 10, or story line completion makes you eligable to expand another specific portion of the house, or attain one of the effects discussed. (separating moghancement effects in different rooms for example)
This would give people the motivation to complete all of these various story lines and quests. For those that have already finished a particular line, speaking to the final NPC in the line, again, would trigger the Mog notice. Or Zoning into the MH, in a nation you got Rank 10 and moved on, would do the same thing.
For those that have finished all of them in the past, this would be additional recognition of their effort, and for those starting out, it would give them something besides lvl 90(99) to work towards.
The amount of MH expansions you get would depend entirely on you. If you are only interested in Gardening for example, you only would need to do the story line that gave you a "Green House" expansion.
I know they are already doing this with the synthetic Atma, but this would add incentive.

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