1. Stealth. If it is called stealth then it needs to be just that. Invisibility is a magical term and is a better term to describe the current stealth mechanics in MMOG's. The only game I have seen with accurate stealth is Planetside and that is a MMOFPS where it actually makes sense is balanced to the game.
Stealth is a scape-goat for lack of imigination in my book. It is often paired with high damage attacks and abilities geared to prevent an enemy from fighting back. If an MMO wants to have any chance at balance it MUST NOT have an ability that allows a class to pick and choose their fights while MOVING UNSEEN around the entire world.
If stealth is a must in a game the counter to stealth... usually a tracking ability... needs to be just as effective. Shadowbane did very good in this regard with its scout class because it offered scouts a place in the PvP game because of a utility skill.
2. Crowd Control(CC). I don't know about you, but I prefer to be able to PLAY a game when I am logged on. Any ability that prevents you from playing your character, using your basic abilities, or completely disables your character is just not a good idea when it comes to balance.
Case in point. WoW's current system. Blind, sleep, stun, fear, and other abilities PREVENT you from fighting back. It is one thing to have a root or slow ability that slows you down... it is another thing to have abilities that PREVENT you from playing. DAoC was a good game to learn from and WoW has failed to learn from DAoC's mistakes. The end result is WoW following down the path of DAoC... constantly adding anti-CC abilities, items, and skills.
3. Lack of utility. Regarding balance... it does not always need to be about damage and healing. Utility needs to be the defining factor in balance. If a class or skill set is designed to be low damage there needs to be equal utility elsewhere.
A good example.... WoW's hunter and warlock. Relatively average damage, but loaded with utility in PvP. Warlocks offer summoning, pet abilities, and so forth not revolved around damage. Hunters have track, hunters mark, and other anti-stealth abilities. The only problem it is a one trick pony and most classes lack utility... like warriors who are pure damage with little other uses.
A big mistake is offering only support classes and skills utility. Damage does not need to be over the top in PvP games. Utility can be the defining factor. Having everyone on the same average damage tables opens a game into the utility aspect. Abilities that are focused around different in game situations that benefit the wise player.
Sadly utility is usually used as a side show to damage and healing.