mine is the PS3 but i figure that the controls are the same. The penalties work rather differently now. I'll explain using the D-pad
Assuming opponents goal is the right side:
Let's say u wanna hit the penalty to the left corner. On the game screen, u would wanna Press UP on the D-pad and tap square. Be sure not to hold the D-pad too long or too short else u'll either end up hitting it way wide or too close to the middle. Same thing for right corner, u'd hold DOWN on the D-pad then tap square.
Now for power, unlike the past PES, the power is not affected by how long u hold the Square button already. Instead, its determined by the left and right buttons on the D-pad. If u want less power, hold left, more power hold right. Now take note: U gotta time it very carefully, holding too long will either end up in a super tame shots or balls that go to the roof of the stadium. Often tapping LEFT or RIGHT is more than enough.
Give it a shot in training and u'll get used to it. I had to resort to it myself when i missed a few penalties in ML and it started bugging me how it work. Right now i'm pretty confident that i wont miss or at least get it on target. If u experiment abit, u can even pull off some cheeky penalties. I've managed to score a few in training by dinking it over the keeper. Makes for a very nice moment hehe.