I've been back and forth with Taelorn on the subject of the Hercules today. I'm not the ship expert and I'm not going to tell you everything he said. (That's two different, unrelated facts: 1) I'm not a ship expert. 2) I'm not going to tell you everything he said.)
Basically, the gist is this: If you compare the stats of a Hercules to the stats of a 4th rate, it's not surprising that you'd wonder why the Hercules would be worth the money. However, experienced captains lucky* or rich enough to own a Hercules tend to find it worth it. Thus the pricing designed to make it rare. 4th rates tend to have exploitable weaknesses that the Hercules (and other apparently crazy-expensive, high-end ships) don't have.
I know that's not a lot of specific info. I'll also throw out there that Taelorn has additional stat tweaks planned for this ship. However, they are tweaks, not redesign-from-the-ground-ups. Hope this helps at least make you realize we are reading your feedback and pondering it even if we don't rush out and implement your suggestions right away - or ever.
*Luck played a key role in folks getting chosen to participate in Beta.