Mercenaries were very unreliable in this time period. After all, they were out there to make money, not to die. Thus, if they didn't like the situation they could attempt to switch sides or retreat. EU3 doesn't reflect this. Make them have lower morale than standing regiments (probably moddable), and possibly even switch sides to enemy in a heavily losing battle (needs programming).
EDIT: Lol I realize this is what was just written above.
Like others have said I also think mercenaries are too cheap.
It's silly they take manpower from your pool to reinforce. Though removing this obviously will make them even better, so something would have to counter-balance this.