It's not an agenda. We had one of the best defences in the league last season, largely due to the partnership of Branthwaite and Tarkowski. Start of last season was the same with Tarkwoski struggling having to play next to Keane, seen the same happen to Mina while he was here as well.
As you say stats can be hard to read at face value, but I know what I see when he plays. He unsettles the rest of the defensive line. He's never been able to form a partnership with another cb at Everton because he looks an absolute nightmare to play with. He's alright facing the opponents goal winning headers and making clearances, but he often leaves big gaps behind him and when he has to turn and move he completely loses his bearings.
Watch an actually good cb like Branthwaite who always looks assured, makes it look easy, knows where to be. Then watch Keane and you notice, he's always slightly out of position, wrong body shape most of time getting caught flat footed or with his back to the ball.
As I said, he's improved a bit this season but we desperately need him out of the 11 imo.