Don't think the tie is over, Madrid are suffering from the loss of Modric, Khedira doesn't really offer much in this type of game, the combativeness he offers(which isn't going to be that great without match fitness) ain't really what's required to beat Atlético as they give you the ball, you really need to just have enough creativity to break the bus. Be it a long range shooter or by tight interplay that focuses on overloading areas of the pitch.
Ancelotti is quite naive for benching Ronaldo, it made no sense as they're facing Getafe next week, not Sevilla or Barcelona.
If I was Ancelotti I'd play Kroos, Isco, Rodriguez, Ronaldo, Bale and Benzema from the outset and use Carvajal+Marcelo from the start and overload the wings. For what it's worth Khedira will offer little at the Bernabeu if Atlético go hyperdefensive from the offset.
Atlético didn't even play that well personally and Madrid made it easy for them, Ramos done goofed and that was a stonewall pen Ramos had his hands on him and hauled him to the floor which you can't do, they nearly scored from Varane's poor ball retention(needs to improve his ball circulation before he starts for Madrid personally even though as a general defender he has it all, the CL final his average ability on the ball costed the corner that Godin scored from). Think the CMs and the wingers did their tracking back job well. Bale also is a bit too one dimensional, you know he's trying to find some space with his left foot to get a shot and if not he'll go down the line if there's space there. Reckon he needs Ronaldo in the team for him to perform at his best at Madrid so Bale gets more space. Ronaldo has a much more fluid style to his play and works much better in the second striker position as he's much better at creating space on the ball with both feet rather than just running on his favoured foot and taking a shot there.