League of Legends. Not quite an MMO, but after the laning phase LoL is extremely similar to instanced PVP in MMOs. In no way are the characters in that game balanced for a 1 on 1 fight. Because each has a specific roll in the game.
Your example of Clerics is terrible because that class was able to fill multiple rolls. Of course it was broken. It could literally do its job as well as the job of another class. A simple example of two for one. If you owned a company would hire one person who could do Job A and Job B, or hire two people for individual jobs but have to pay them the same wage as the single worker? You take the former because of the inherent and constant benefit.
But your stipulation that a balanced team is the best team stands as proof that that the game is designed around 1 on 1 is completely and totally unfounded.
You are using a mathematical school of thought in that one player will cancel out another singular player on the other team. This is not how competitive situations work. In fact arguably the main universal goal in any multiplayer game is to create a number imbalance in your favor and then take advantage of the imbalance to defeat the other team. In other words, your team should always be trying to maneuver yourselves so that you outnumber the enemy team in any skirmishes.
This is not just isolated to instanced PVP in MMOs. At a competitive level of play, all team multiplayer games are about this single concept. Whether it be Halo, Call of Duty, Quake, or Battlefield, you are trying to win the numbers game. As such, playing as a lone wolf is arguably one of the most detrimental things to a team.
Except when it is part of a greater strategy. That is the lone wolf's role. To be used as a pawn to set up the larger trap. Maybe your Starcraft teammate has sent a small scout team to lull the enemy into a false sense of superiority and goad him into a trap. Or maybe your single Operative has stealthed around to pick off a single healer to tip the odds in a fight. The fact is that competition is about doing something to create an advantage for you and a disadvantage for the enemy. It just so happens that if the team size is smaller, the more powerful a simple numerical advantage will be. Furthermore in no way is this limited to simply video games.
Basketball, football, soccer, hockey, whatever. Almost every major team sport revolves around trying to create mismatches against the other team to gain a massive advantage. In football defense blitz linebackers to bring more guys in an attempt to sack the quarterback. It's the quarterback's job to know that in his area he has an unfavorable balance by having less blockers than rushers, but that means the defense has now conceded an advantage to the receivers so he has to get the ball to them quickly to take advantage of the new situation.
In fact the objective of creating mismatches is the driving force of sports. And they do not simply have to be numerical. In basketball, teams on offense try to manipulate the defense's rotations by passing the ball around until they get a match up they like. An example would be forcing a center out on the perimeter to guard against a three-point attempt leaving someone much smaller to guard the post allowing for an easy lay up or alley -op.
Or the mismatch created could be catching a squishy consular away from other players. The fact is that NO TEAM BASED GAME IS BASED AROUND A 1 ON 1 SCENARIO. This is completely counter intuitive to the way team games are played. Team games are about using the strengths of different people, classes, whatever to make up for their weaknesses. The sum is greater than its parts. And until the MMO Trinity is destroyed, each class will either have one of the specific roles or be a jack-of-all-trades.
Even if you were to distill the classes down until each was exactly evenly competitive with the others you would only be reinforcing the strategy of a numerical imbalance. In first person shooters in which there are one or two "best guns" it is both an extremely common and effective tactic to isolate and then eliminate the enemy because you both have the same advantages and disadvantages so you must create using the only dynamic variable left: number of available players.
However (ideally) in MMOs, there are distinct separate classes that have distinct strengths and weaknesses. So in one situation a certain class may shine while in another situation a completely different class would be better. There is (or should be) a class that is though to kill but isn't capable of pumping out obscene damage. A class that can just absolutely unload and destroy someone else, but is nearly useless outside that one instance. An AoE/group healer. A single target healer. A class with good mobility but no absolutely amazing combat abilities.
By having these unique positions you greatly increase the complexity of the strategy available to the teams. To design the game around 1 on 1 fights would be to destroy the innumerable small strategic battles that are constantly happening all around a Warzone. In fact there would be little difference between Call of Duty and this game in terms of competitive strategy if that were to happen. Of course there would be differences, but if the classes are all "balanced" just like the guns in Black Ops were balanced, the game would simply devolve into who attacked whom first.