I dunno, I think there is some places you could criticize him in that he couldn't beat Atletico Madrid in these past two seasons and he won the CL thanks to an arguably miracle Ramos header in the 3rd minute of extra time. Atletico had Real's number for so many crucial matches including the away 4-0. Real also struggled a lot against Valencia and only got one point out of them if I remember correctly. They did split the two league games with Barcelona, but Barcelona won the game that swung La Liga more into their favor.
I think Carlo also overworked Modric and Kroos and the replacements (Illaramendi, Khedira, and Lucas Silva) were all not up to the standard to fill in the space that Alonso vacated or just weren't really given the time to be rotated into the squad. When Modric went out injured, Real's midfield really lost a lot of quality and were forced to use Ramos in the midfield.
He deserved at least one more season and a transfer window to find more midfield / defender depth, but that's Perez for ya.
Rumor has it that Beneitz is gonna be the replacement, but we'll see I guess.