Well, some fleet designs do well against others, and some completely fold. It could happen that a bomber fleet goes against an almost completely AS design, and then do very well against the other 2 match ups. Granted, 10/0 0/10 10/0 is hard to conceive, but it's not impossible. I've heard the Clonisher described as an 80/20 list, being that it decimates 80% of the lists it encounters and folds against the other 20%. So even if you are paired with your equal in skill, fleet design (and objective selection) can negate your ability to compensate. In which case it would be the player's fault for developing a lopsided fleet, and that could happen in a tournament.
Then I would argue that it depends on how you define player skill. I would say what decides skill is the following:
1. List selection and the choices you as a player make in building a list and knowing the capabilities of your list(requires playtesting)
2. Knowing the capabilities of your opponents list (requires playtesting)
3. Learning when to press the attack and go for the jugular when you are in a dominate position, or learning when to try to mitigate and hold your opponent at bay to fight for a mediocre loss/win or draw. (This skill is acquired by doing the prior two)
In which case the Armada setting and tournament rule set provides this the best given the time requirement and player involvement. Generally speaking the player that is most skilled will win a tournament nearly every time provided he learns to excll at the three things mentioned above. Which again requires studying games and playing games. That will ultimately be how you overcome the perceived Rock/Paper/Scissors in the game.
I would like to add that even if we can solidly prove that there is a paper/rock/scissors to the game (which I tend to believe to some extent that there is). In Armada paper does not automatically 10-0 Rock. And when flotillas come out I think there will be a case of paper/Rock/scissors/lizard/Spock.