Ships of the line should be faster at the high end than scout ships, but they should take much longer to accelerate to that speed. The idea is that if you let a ship of the line chase you in a straight line, you've made an error.
We are not going to return to the point when scout ships were faster on the straight away than ships of the line. We moved away from that specifically to give large ships a chance of engaging smaller ships. However, the top speed disparity is too great right now, and we're working to addressing that.
No one should be able to pick all of their fights. Ships of the line, with their slow ramp up speed, poor maneuverability, and limited speed at some wind angles, have built in vulnerabilities in that department. If small ships were faster than them on the straight away, they would never be able to engage a small ship. At the same time, there's no question that right now the speed of several frigates is too low. We're increasing it for just that reason.
There will likely be a post later today (possibly tomorrow) with more discussion of some speed changes we're making. I'll be sure to drop a link to that in this thread when it goes up.