I was initially annoyed with the auto add of skill points, but then I realised the changes make the game more realistic.
Players in real life would gain skill increases when training and playing matches and these would be immediate. We can still set which skills the player will focuses on and these will then be auto applied after training or playing a match. This makes absolute sense to me and I think it actually makes the game more realistic where a manager will say which areas he wants his player to focus on and then they improve in those areas through training and matches.
I think stockpiling skill points as many have done in the past is actually cheating and effectively treats players as robots rather than people.
What I would like to see is a training report so we can manage our training more effectively. The report would be a message either daily or after a match / training which details the players that have improved and the skills they have improved in. Without something like this it is impossible to see where players have improved.
Ideally as a second phase to this, I would like to see a graph of players average skills per group over time i.e. a graph for defensive skills, a graph for attacking skills and a graph for physical / mental skills. This could be accessed by selecting the skill grouping from the individual player screen. This would allow us to track improvements over time and manage this more effectively.

I agree with others that there is a need to see the percentage for condition and morale since the new method is not accurate enough.

I also agree that the UI is a little difficult to use on a mobile phone.

Putting these into order I would say:
Severity 2 - add a training report; without it we cannot manage the training
Severity 3 - add skills graphs to players
Severity 3 - display percentages for condition and morale
Severity 4 - make UI a little clearer