As it stands right now, I personally feel that CCP is making a mistake by trying to force player run markets into Citadels by making the taxes higher in NPC stations.
That being said, even I think there will be a huge issue with the market function of the Citadels that will cause a massive shift in the economy as a whole (even if they reverse the tax changes).
I am aware that this issue mostly affect high sec, but since the markets everywhere are driven either directly or indirectly by Jita/High Sec, this will impact the rest of the game.
The potential issue surrounds the use of "Region Wide Buy Orders".
Right now, region wide buy orders are used to help someone buy materials across a whole region with one order instead of going to each station and putting an order up there. This also allows someone to sell their stuff from more stations. The trade off is usually a lower price for the seller. This is fine as the risk is fairly low for the buyer because you can get to any station in high sec and low sec. Yes, null sec is different as you can get locked out there, but that is already a well known risk. Market volume alone makes this more of a high sec issue.
However Citadels bring with them a unique change - The ability to decide docking rights.
What will be done (we know someone will try it as this is Eve).
You would put up a Large Citadel up with a market hub. You make it so ZERO people besides yourself, alts (if you trust them), and your friends/corp (again, if you trust them) can dock.
You then go a fill EVERY system/region wide buy order you can. Once you have filled them, you place a station/citadel wide-only buy order that is lower than what you paid for.
The person comes to get their items and finds they can't. The only options they have are:
- Get someone to war dec you and kill your citadel (could be costly depending on how strong a large citadel can be in high sec)
- Hold onto the items till someone else kills the citadel (and then pay to move their stuff, because if I was going to do this, I would put the citadel in a system with no other NPC stations

)
- Re-list the items at your citadel on sell orders (but again, if I was doing this, I would put the citadel taxes very high)
- Wait for someone else to put up a region-wide order and then sell to them (a new person is now holding the bag)
- Sell the items to you for a loss.
- Pay you for docking rights (who will trust this?)
- Pay YOU to move their stuff via courier contract
- Never use region wide buy orders again.
This will make the market less stable as everyone in the game will have to ask themselves whether or not they have to worry about docking rights where ever they go to buy stuff.
There are a few other ways to game the market, but the one above is the easiest to see.