If they would like to keep the current system in place I think the easiest way to make it more fun/convenient is to add a far more advanced function. By this I mean (If you ever played EVE you know what I mean.) making the search button far more advanced, then making it possible to place "orders". This system will allow people to make gil simply by shopping around and traveling. When you place a buy order you simply set the time limit and add in some extra money as incentive for another player to deliver it to your home/retainer where you pick it up. This will make items more competitive and also make a great marketing tool since each area will have completely different market values (I think this is what they were aiming for), while at the same time adding another "job" people can pick-up to make gil.

Obviously it is far more complex but I think you will get the basic idea of it. This won't fix many of the issues that have been listed but it at the very least will add a layer of game-play while at the same time adding a simple option for those that don't want to bother with browsing retainers to simply pay for another guy to deliver the said item for the said price.

This will give a purpose to having the physical retainer placed somewhere. If you don't want to jump from retainer to retainer, zone to zone, trying to find the best price/item then you don't have to. Simply pay someone else to do it for you and have it delivered. Again, this is not a broad band-aid to the current issues, simply an idea that will help or be more entertaining with a specific problem.