So I'm going to keep this short and sweet. The current problem with the way that Chocobo Raising was implemented was that it requires gardening, keyword here being -requires- it. The best fix for this would be to add a purchasable item that doesn't provide a buff but can be used to at least train your chocobo, however an even more ideal solution would be to add personal garden plots.
Anyone who has ever played Final Fantasy XI probably remembers flower pots in it, those things people filled their rooms with to plant seeds in and grow all kinds of crazy plants! This is fertile soil for SE to use (pun intended) where they can add items that have 1-3 garden plots as an indoor item that you can set somewhere. This would solve the current issues easily as well as make gardening more viable.
The primary issue with gardening really comes in when you have large FCs who all want to train their Chocobos but don't have enough to make vegetables for everyone. The issue arises where they need to decide, do we use every garden slot for making vegetables for people, or do we use only some while using others to make things like jute? If we make vegetables who do we give them to? What if people want to plant the seeds to grow the new Mandragora minions? Probably any other number of problems as well.
In short, with private chambers and way more things that require gardening, they need to add an item that lets players garden themselves in the privacy of their own "homes."