Mkhitaryan was bought to be the right winger I think and he suits Mourinho's system perfectly for that. He played for Dortmund on the right with license to drift inside and that's how Mourinho likes his wide players to play. Mata on the other hand doesn't suit Mourinho because of his lack of mobility, and while he is an effective player, he won't be a long term starter option because of his limitations. Yes he can have great games on occasion, but he'll always be a level below the likes of Silva/Ozil/De Bruyne/etc because he can't run with the ball and drift past players. Isco on the other hand is exactly that type and has huge potential, just needs the stage to fulfill that potential, as he is already a very good player. He has shown really good form for Madrid before, but it's tough to get in when they have Modric/Kroos/Ronaldo/Bale playing in the 4 around the striker, in front of a holding mid. Even having James Rodriguez on the bench to compete with. There is a perfect spot open in our team for him, next to Pogba, so he would easily slot in there. Having someone like him in the middle for us would be perfect for our attack, just like how Silva was for City since he signed for them. Very similar type players, and will let us have a nicely balanced midfield 3 (or the 2 more advanced ones, as we still need to sign a holding midfielder).
You are saying warming the bench at Real Madrid like it's a huge criticism and a reason not to sign him, but what were Thiago, Fabregas, Alexis Sanchez at Barcelona before they left? All squad players, but players who are world class players and just need the games to show it (fabregas is now like Rooney of course and has declined, but that doesn't change what he was). James Rodriguez is also a brilliant player. Just because a player can't get in a team who has a midfield that has literally the 2 best creative and controlling midfielders in the world, doesn't mean he isn't a brilliant player himself.
Also just look at our possible team with him:
Ibrahimovic
Martial Pogba Isco Mkhitaryan
Carrick/Herrera
Without him if we put Mata in his position, it just isn't as balanced and isn't a viable option against the best teams because of Mata's lack of mobility. Yes he works hard and runs a lot, but that doesn't mean he can play in a midfield 3 like Isco can. I would want to see Mkhitaryan there, but then we need to sign a right winger and it's not like there are many of those around. Mkhitaryan is equally good on the right, so Isco coming in the middle would be a very attainable but potentially world class option.