Some general suggestions
1- About the new changes: How about not hurting the fan kind of stuff if you sell a player / week or 2 weeks. What I mean is that it would be nicer if there wasn't any specific effect on your next game if you sell just 1 guy for a certain amount of time to rebuild your squad.
2- Sort feature for bookmarks. I sometimes look for certain kind of players and bookmark them. However, since it only sorts according to names, it becomes a mess about their auction end times. It would be nice if we could sort bookmarks according to auction deadlines.
3- TL features: Searching players according to their potentials too (i.e. min or max potential) would be nice. In addition, it would be good if we could search for more than 4 attributes at a time if feasible.
4- Current bids page: Maybe it would be nice if we could see the players we put on the transfer list and their deadlines before any bid is made for them.
5- Offense suggestion: How about having offensive tactics such as "fast-break" or choosing a specific "target man" or being able to tell a player not to shoot the ball etc? I think the availability of additional strategic options would be nice.
6- Stamina thing: I think instead of being a separate training regime, it should be something that is dedicated each week. Even though I got this idea from hattrick, it seems more logical to me that I can't imagine a team not getting stamina training in any given training week. The dedication amount can be subtracted from the total effect of the specific training that is chosen. Therefore, it can create a trade-off in dedication amount.
I guess that is it for now. Maybe some of them are not possible to do but I wanted to suggest them anyway :)