why dont you move the shipyard closer to one of the planets ?
I' don't think it makes a difference. One of my shipyards is one hex away from my first colony. The other 4 sponsors vary in distance from 14 to about 100 (last isolated colony). There is 0% distance decay on any of them.
unless you have the traits that reduce distance decay part of the reason it takes so long to build anything will be that your planets are so far away
It does take a long time to build a large ship; I just assumed it was because I was concentrating on tech instead of manufacturing. I've just started researching manufacturing centers. When I started my first game, I assumed it was like GalCiv 2 and had a shipyard at every planet, but THAT seemed to slow down building even more, with just one sponsor. Maybe I'll try more shipyards, have the closest planet be the only sponsor, and then switch major manufacturing sponsors around to the ones where I most urgently need the ships.