On my recent visit, I noticed the following changes that increased wait times:

1- they eliminated the single rider queue for Soarin.

2- they linked fastpass between the two parks. Before you could have one at Disneyland and one at DCA at the same time and as long as you were able to hop back and forth, you could ride more rides. Now if you have one at DCA, you can't have one for that time period at Disneyland or vice-versa. It takes away one major perk of having a park-hopper pass.

3- they added fastpass to Midway Mania and the Matterhorn. Now both rides how much longer standby lines. I liked to ride Midway Mania a few times early when the park opened and a few times late at night, trying to beat my high score. (My normal score is usually > 215,000) With the addition of fastpass, the wait is now greater than an hour, so multiple rides early or late with a short line is a thing of the past.