Some skill change suggestions.

Nebula, Wither, Leech, Flames of Insanity, Psychic Lash: These skills could do a little less damage but ignore armor. This solution balances the skills and makes them useful for either regular enemies or bosses.

Increase Mass: This skill could reduce damage by a % instead of simply adding armor. That will allow the skill to keep up with ever-increasing armor rates.

Growing Rage: This skill could last 5 seconds and recharge in 20. Same ratio, but players would be more likely to use it instead of fearing the 60 second cooldown.

Empathy: If Empathy is already active when cast, this skill could give 1 tick of instant healing instead of simply resetting the timer. That would allow simultaneous casts to compliment each other and also encourage strategic casting.

Revive: The cost and range of this skill could stay the same, but points in this skill could instead revive characters with 10% and up to 60% hp/mana depending on skill level. This change would encourage support engineers putting more points into the skill.

Protection: If Protection is already active when cast, this skill could add a 5 second buff that reverses the next single damage taken by a character, and instead heals that character for 10 and up to 60 hit points depending on skill level. This change would allow multiple casts of the skill to compliment each other.

Sonic Boom: This skill could cause Pain to detonate instantly. This change would give this skill more utility and force more strategy.

Lurch: This skill could break a character's autoattack if the enemy is knocked back the full length of the skill. That would prevent the character from continuing to attack/use skills on an enemy beyond his reach.

Blur: Instead of increasing dodge, this skill could increase the operative's running speed by 5% to 30% depending on skill. Same duration and recharge. This change would allow some operatives a hit and run option while not directly affecting survivability.