Matchmaking counts your top {x} characters where {x} is the number of characters per squad * number of defensive squads * 2 (defense+offense).
For GACs including a fleet zone it seems likely that the same formula is applied to fleets and then the two numbers added together. I have not seen anyone produce hard evidence for this as yet though subjectively it would explain the general balance of my matches: I am more invested in fleet than many of my opponents and they tend to have more top-end squad GP though not always wisely spent in GAC terms.
So if you want to improve your GAC matchmaking situation, you need to be thoughtful about which characters and ships you power up and how far you power them up.
Powering up one squad to high relics for example while neglecting the general balance of your roster will draw tougher opponents at matchmaking time and wont necessarily help you in GAC or elsewhere.