Hello, I'm not sure if these suggestions will actually be taken on board by who ever makes the decisions but here we go..
(I use the Android phone app version for future reference):

Physio centre -
the physio centre is a very good idea as I like being able to apply multiple rests to multiple players, I would suggest that it also become possible to do this with morale boosters and treatments. Also a minus button would be useful as if I am adding several rests to a number of players I but make a mistake, I have to cancel it for all the players and start again rather than just press the minus button for whoever I accidently gave an extra rest to.

Youth players/loan system -
It is strange that it requires time cash and tokens to create a youth system that will only produce either mediocre players for free or decent (but still not that good) players who cost more tokens than it would cost for me to go and get a better one on the auction(even though I have my youth system maxed out). The better youth player that comes through is far too expensive for the level of skill he has, and the new training system means he doesn't even grow as fast as he used to. (ideally i'd like all youth players to be free or at least cheaper, like 3-9 tokens).

Loan system -
I propose a system where managers at higher levels are able to loan their youth or even just their lesser able players to managers of a lower level for a season or half a season; the lower level manager benefits from a temporarily better and deeper squad, and the higher level manager can receive an improved youth product afterwards (if they get game time and are trained whilst on loan). Rather than have to create a whole new interface page for this, you could allow loan requests from managers to others in their friends list.
You could even charge both managers a few tokens each to use this service (if you must...).

New training system -
I'm not 100% sure about how fast players improve with the new training system but I feel like it's much slower, and do the younger players still advance faster than the others? Some aspects of the old training system were good and should maybe be implemented into the new one like individual training - I only have 2 goalkeepers so the goalkeeping drill is rarely used as I train all my players together to benefit from the bonuses.
It seems as though the emphasis in this new training is more on bonuses rather than increasing player skill level, which isn't good because I can still end up drawing a game with a lesser team despite having the max bonus, even if I won i'd rather have done it because I've trained my players to be better rather than trained them enough to get a high temporary bonus..

Negotiations -
Lastly it is a good idea that people can offer me tokens and cash for my players outside of the auction, but why only players who are about to go up a class? I get offers for players I don't wish to sell and have never had any of my offers for others accepted.. Surely allowing the managers to choose who can show up on this list will make it more useful and people would use it more. Also why not separate the cash and tokens on this system, for example if I offer 9 tokens for a player and 4m cash (which turns to 5 tokens after the charge). Can't I increase the amount of cash I'm offering without Increasing the amount to of tokens and vice versa?
I think this would benefit the seller I'd they are in need of cash for players/construction but don't really need more tokens at the moment and the buyer could try and secure the player using which ever one he has in abundance (or a combination of the two that he chooses).

Just some thoughts of mine I'd like someone to hear, I welcome all comments. Thanks for reading