In order to effectively have special abilities in a game there must be some form of limitation available. This is typically done with either cooldowns or a resource system. My first idea is to utilize a resource system called "Action" (referred to as "AP" in the game's UI). Most abilities will cost between 20 and 60 Action, while the player will regenerate 10 per round. Certain professions (especially those who rely more heavily on specials) will receive additional methods of replenishing Action.
I think an overview of the general idea behind the specials system will help explain the Action system. For starters: not every profession will have to use specials regularly. Most of the Adventurer (and its elite variants) specials are being designed for usage in emergency situations or during an opportune moment. On the other hand, the Mercenary (and its elite variants) will be encouraged to regularly utilize specials. The Warrior's special ability kit is being designed around the idea of "melee is at a disadvantage". Because of this a player with really high stealth or simply good tactics could theoretically minimize specials usage as a Warrior.
The second point is that there will be a fairly limited number of special abilities for any given character build. At the highest level of play a character can expect to have around six abilities, each with a defined usage. This prevents two things: ability overload (literally just having too many abilities for one player) and keeps all abilities relevant. It is also good from a design standpoint as it will be easy to ensure that Bounty Hunters and Commandos play pretty differently, for example.
The third point is that "normal" attacks and plain player tactics will stay relevant due to the relatively slow regeneration rate of Action. For most professions you won't be able to use specials more than once every two rounds, assuming you constantly utilize your cheapest ability. Specials will definitely have power proportional to their cost, so firing off a 20 Action cost move every other round is probably not going to be a sound tactic in most scenarios.
As a final point it seems worth mentioning that specials will scale with attributes. A Commando with high a Technical attribute will be a serious threat indeed. This will insure special abilities remain relevant no matter how long the game ends up lasting.
As per usual, the concepts discussed in this article are still at a fairly embryonic stage. But I am fairly comfortable with the general idea of Action and special abilities, so you can expect some variation of it to make it into the prototype.