Finally you have the mechanics themselves. If you have the other areas under control you can still fall foul of your games mechanics themselves. A spreadsheet might tell you that two abilities have an equal DPS output for example. However if one of them is very simple to execute in the game and the other is not they aren't actually equal. This is where a lot of the class issues crop up. Sometimes this is intentional on behalf of the designers. They may want some classes to be more newbie friendly to allow less skilled or experienced players to participate, likewise they might design a class to be rewarding if you get into the complexity of their skills, and one may not have a higher maximum output than the other.
This is the difficult area where rewarding players can be difficult, some players like a challenge some don't, but those who want a challenge generally want rewarded more than someone who doesn't and depending on your design that might not be beneficial (due to the maximum values we talked about earlier). We face this issue all the time in Age of Conan for example as the game was designed to have the casting system to be inherently simpler to help support players who did not want to deal with the faster paced melee combo system. This makes an inherent imbalance that is supported to some extent by the original design. For us in some way it works, and achieves its objective without slanting the players only towards casters (most players in Conan still play melee classes despite the mechanic imbalance) in other ways it does frustrate experienced players who would prefer everyone was equal. It also becomes more apparent when there is an actual additional imbalance when we don't get things quite right with any given skill or ability.
So method number three is how you use the mechanics themselves to affect the balance.
Feedback on Balance
Lastly it is also worth mentioning player's perception of balance and how it affects feedback and discussion of balance. Players have an inherent bias towards their preferences (in particular with PVP) and often focus on only the areas where they are at a disadvantage and don't dwell on the areas where they have an advantage. It doesn't always make the feedback invalid but it does mean you have to be careful about not swinging the balance pendulum too far when you make changes.
Don't get me wrong you get good feedback, often a lot of good feedback, from players but you do also have to weight that against the data you have and the systems you have in the back end controlling the budgets and recognize the inherent bias that can exist in most balance feedback.
For example there is definitely and on-going discussion about the balance of Melee and casting classes in Age of Conan, and we definitely still have some ongoing things we will continue to tweak in that regard. The players that provide us with the most feedback clearly see that it is easier to maximize the potential of a casting class rather than a melee class (due to the mechanics aspects as I mentioned earlier) and that is the case. It is easier, and offers and easier option, but the other side is that melee is still very viable and in skilled hands equally powerful at what their role is on the battlefield, the issue is that with two players of equal skill the caster is easier to master. In other games it might be the other way around, it all depends on those mechanical aspects we mentioned earlier.
So if you were to ask someone active on our forums who is part of the dedicated community they will most likely tell you that it is quite a severe imbalance between melee and casters due to that, but on the flip side, melee classes make up all of the top four most played classes in Age of Conan so it also doesn't effect things to the point where any kind of majority feel compelled to 'reroll' as the easier option, even if the acknowledge it is easier.
Our balance in that respect probably isn't quite there yet and we acknowledge that and work on it, but it also isn't as far away from being well balanced as a vocal hardcore player would have you believe. That's the challenge of working with an MMO. After all if you ever do achieve a mythical 'perfect' balance you would most likely see an awful lot of complaining about it because everyone, regardless of class or class type, would always have a good chance of losing...and that brings us back to my opening point. In an MMO that 'perfect balance' probably isn't what you are looking for it, rather it is a weighted system that allows for winners and losers that rewards the player for their knowledge, timing and targeting. Down the years I have watched many great PVP players and the one thing they all share most of all is the ability to pick their fights and see their opportunities and their almost uncanny ability to know when to chase and when to run away.