This is ALWAYS going to be an issue in games that don't want to make every character made homogenized. There will always be some form of efficient setup as a result. Short of a debuff to power for overusing one specific class in a party, or requiring use of specific classes to do something, it's almost impossible to guarantee balance for any one thing.

Doing any of these things to prevent the "preferred" setup just makes the game overall less fun for everyone. Sure it'll get you into that event/fight/whatever easier, but it'll exclude others at the same time, almost to a degree of necessity. "Sorry, we can't invite you because we already have a <insert your class>" or "LFM need <least used class> so we can start the fight".

From the developers standpoint, you ask for the impossible when you ask too much. You don't want homogenization, you want there to be prevention of preferred setups that excludes your preferred playstyle (even though outside of the preferred, you still do fine), yet you still want them to treat things as though it were.

I would not be surprised if folks actually think it can be done in one days work to balance the game out. Thinking that it takes no thought at all for developers to, for example, make any fight in the game automatically adjust the difficulty according to party member classes, levels, gear, etc. That it's just a simple matter of typing "balance" in a single line of code. That'd be awesome, and probably would put a large number of people on an unemployed list, but that's not how it works.