A lot of changes have been made, most of them in match engine, and some in the user interface to help easier navigation. Also the back-end code has been optimized a bit for faster performance of the website. It is a lot if we list all of the changes here, so only the major updates are listed below.

Match Engine Update
Major changes have been made to the match engine, especially in the set pieces. Smaller teams will no longer find it easy to score from set pieces and cause upset victories and such cases will be very rare.
Experience gains from matches has been increased slightly by around 10%, since we noticed that players were gaining experience at a very slow rate.
Fixed few bugs where players other than those assigned for the corner/freekick roles were taking it. From now on, attacking set pieces will be always taken by the assigned players.

Minimum Transfer Listing Price
The minimum transfer listing price for players has been reduced from 75% of their value to 50% of value.

Competition Prize Money
From Season 3, all teams participating in a knockout competition will receive prize money.
The runners up will receive 60% of what the winner gets, the semi-finalists get 60% of the runners up and so on. Please see the Advanced Tutorial for more details.

And that's not the end of it. We will continue to improve the game, and you can expect much more in the coming seasons.
Hope you enjoy the game!