Good suggestions, Jubz and welcome to OS!

The transfer market is in need of a lot of work. You can't even see what players are moved after each window in 08. Here are some additional ideas I have for improvements in no particular order:
1.
Bosman transfers in the January window. This was in WE for the PS2 and was well implemented. You could negotiate a free transfer with any player in the last year of his contract during the mid-season negotiation period and if successful, they would join your squad for the following season. Not incredibly common, but it 'is in the game' so it should be 'in the game'...
2.
More variety/logic in terms of what teams bid for a player. As it stands now, you'll usually only see teams from your league bid for any players that you list, with the exception of the occasional odd-ball offer from some tiny club that would never make such an offer. I think I had St. Mirren (Scotland) make multiple offers for Alex Hleb in my Arsenal MM. There should be more of an emphasis on the size/prestige of the club in relation to the quality of player in question, as well as consideration of what nation they are from. The latter would be cool for players who are past their prime who often return to a smaller club in their home-country to finish their career (recent examples: Ronaldo back to Brazil or Makelele to PSG) or if I wanted to sell Luca Toni from Bayern, there should be Italian teams lining up at my door, not a few German doormats...
3.
We need a bidding system that pits teams against each other. I know past versions of Madden and NHL 08 have a system where you can see offers from other teams for free agents. Anyone who follows professional soccer's transfer market knows that rarely is one team involved in any potential move. If I want Klaas Jan Huntelaar, not only should I have to meet Ajax's value, but I should have to exceed the offers of other teams for wages & transfer fee...
4.
The inclusion of swap & swap+money transfers. Another one that isn't terribly common, but fresh in my mind with the current Gareth Barry saga. We should be able to offer a player for player or player plus cash proposal. Not to harp on the subject, but this was also in the WE series on PS2...
5.
The wage system needs to be completely re-done. At the start of manager mode you can successfully offer every player on your roster a contract extension for a significantly lower salary than they currently are making. Umm, yeah right! From time to time players should want more money and demand a transfer if they don't get it. Can you tell I'm an Arsenal fan?
6.
The CPU should actually use any players they buy!!! No discussion would be complete without this dead horse-like point. Had to inlcude it...
Overall, FIFA needs a more robust, interactive and life-like transfer system that takes into account team factors, player desires the various other elements that influence who goes where. As of now, it's more or less deciding what player you want, accumulating enough money and buying them. There is no sense of competition for someone's signature, which is really what can make all this transfer business so enthralling (or frustrating depending on who you support). I think an interface more akin to the recruiting system used in college football & basketball games (interest, pitches, promises of PT,etc) would more accurately reflect the challenges of successfully acquiring players. That is all...