I think the capital ship problem is largely due to the crappy default FOV, which not only makes the bigger ships look too small but also creates several other strange effects for things appearing near the edges of the screen, like making background planets look elliptic and stretching out ships very close to you to the point that they actually seem to move relative to the background when you turn. It seems that setting the FOV to 0.3 or 0.4 fixes all these things and really makes a big difference, but it has the side effect of making the backgrounds look way too big and blurry. Is it possible to have the background sphere/skybox adjust its distance based on the FOV, or would that just put the elliptic planet issue back in?
As for the actual model sizes and scales, it already takes about 10 seconds to go past most destroyers in an average speed fighter and cruisers are much smaller (maybe 1/5 of the size), so it makes sense that you should fly past those fairly quickly. There is the whole issue of many of the fighters and bombers being too big (their models, that is, not the visible size ingame), but I'm not sure how those could be changed without significantly altering the gameplay.
Apparently, the best way to address issues of scale is to go direct to the source, and change the scale of the game. Everything is 20 times too small, but the simplest solution, to resize them all up, would need code changes to tell FS that a meter is now 20 times bigger - not easy, nor particularly fun to code I'd imagine.
Well that wouldn't really accomplish much, since the relative scales between everything would remain exactly the same. You would have to change some things and not others to see a difference, but that would screw up the gameplay in existing missions.