1) - Keep the wards but expanded them to include buying straight from item search list but maybe add an extra 5% delivery tax to encourage you to actually go into the ward to pick the item up. This would also help remove a little bit of gill from the economy.
I am against buying from the "list counter" because of the overcrowding and Lag it would cause. I would like to be able to track more than 1 item at a time and it needs to track which Wards the Retainers are in. I like the idea of having the lowest price a diff color.

2) - Add filter options and a better layout for the item search lists. Filters for thing like rank, class and so on and then sort them in order high to low and so on.

3) - Also show +1, +2 +3 items in the search list and so on.

4) - Add price history please. To make it so it is more difficult to exploit could you make it so you can see price history for last 20 sold, average price over the week, month, 3 months and so on. That should make it easy to spot if someone is trying to jack the price up or crash it on an item I think.
These are all needed tweaks I agree with, except on Price History maybe all we need is 1 "Average Price". If a real price history is used I do not want names given. I have personally seen and been a victim of "griefing" because someone is selling an item "too high" or "too low"....whatever, get over it. In an open economy people will overcharge and undercut depending on the market and their own "profit - effort" margins...it's called Capitalism.

5) - Add an Item Seek Search so you can have look and see what items people are looking for and sell them if I have them. I also want my retainers to be able to Seek for items even if I currently don't have any of them. It seems silly that you can only seek items that you already have as most of the time you wouldn't be able seeking them if you had them. I believe the Item Seek List will be a big help to give the Wards a much needed boost.
This is a good suggestion. Perhaps the "Item Seek" could be a counter outside the Wards so we know what items are hot and what peeps are willing to pay.

7) - Maybe also link all the wards from the other cities. This could help ease congestion in Ul'dah's wards and maybe help stop them crashing so much.
This is where your tax idea could work. Go ahead and link the 3 cities wards but you have to pay a tax if the item needs to be "transported". The NPC's that used to be in the wards could handle these transactions.

8) - Allow retainers to be called at camps so we can drop off gear or grab something we have stored.
This sounds fine to me but giving items to my retainer is cumbersome anyway so I would rather just have a Mailbox to send several items to my retainer at once.

9) - Maybe you could have MW counters in the camps and hamlets, where you could buy items straight from the list but you would have to pay a 15% delivery tax on the item.
I'm fine with this too so long as it doesn't create Lag in those areas.