This matchmaking is a great example of how you can't please everyone.
Initially it was matched on pure GP. This meant that players with low of low gear level 85 characters were paired against players with a bunch of level ones and better g12s to make up the power difference. Obviously the "fluffy" players complained this wasn't fair.
Now the game just looks at your top 50-90 characters (based on gp range) and pairs you against people with similar GP in that active range. If every attack takes a single squad to win, no other characters are relevant.
However in this scenario, players who were top heavy and previously had super easy matches now play against people with similar top range characters - and if a player has many more g12 toons, those are considered irrelevant for matchmaking.
In any scenario there will be players who have an advantage and some who are at a disadvantage. I know my matches got a lot tougher. I'm actually paired against a player with 300k less GP than me and I think it's going to be a really tough match because of his roster. All those extra 7* toons I won't use are truly irrelevant.