I definitly agree that the pirates need to be tougher. When I play against the AI, late game I will get into huge bidding wars to see who can put the most bounty on someone. I put some on him, he puts a little more on me, so I put more on him. Eventually, it gets to the point where I put over 500,000 on him and then the pirate raid. With this much bounty, the pirate raid should be a fleet of EPIC proportions. Not a couple of weak little ships.
My suggestion to appease everyone, those who want the pirates to be stronger and those that don't, is that when you turn the pirates on or off, there should be levels of their intensity. Instead of just "on" or "off," how about off, low, normal, and high levels of pirate activity in the area. Higher level equals more pirates in a raid.