To be honest, this is a match that is no longer a priority for Madrid. I see that the starting XI that Ancelotti implemented was really just to test the mentality of some of his young players. I don't see this match being that special for Madrid and maybe it was very good for Villarreal because it wasn't easy and they were able to equalize the score when they were far behind.
Ancelotti will definitely evaluate the performance of his young players to strengthen their mentality next season and I think Ancelotti is also very satisfied with his team's performance.
Since Real Madrid has won the La Liga title this season already and they have qualified for the UEFA Champions League finals, Ancelotti will not want to risk his best players getting injured. Ancelotti has been using Real Madrid players, who don't have playing time, to play some of their remaining matches, and they are pretty well performing. Villarreal only equalizes against Real Madrid because not all of their starting eleven played that match against Villarreal. Ancelotti wants his starting eleven to have a good rest so that they can perform well against Borussia Dortmund in the UEFA Champions League final.
Ancelotti playing second-string players and giving time to players who rarely get playing time is a very good decision. Because apart from being useful for providing experience to the players themselves in the field and making them better prepared when needed. I especially like Arda Guler who made an extraordinary contribution. I am sure this young player will be a main player next season. Because his sharpness as a front line player is beyond doubt even though he is still very young.
And yes, currently Real Madrid's main priority and focus is the UCL final. So giving the main players more rest time can hopefully keep the players in their best condition when the UCL final arrives. And it is very risky to play the main players in the match before the final.