I was initially very excited by shipyards, but I think as implemented they are not reaching their potential. I think there are two main reasons for this:

1) Range penalty too severe. One of the exciting prospects when shipyards were announced was the idea of dropping them just behind the front lines to eliminate the tedium of bringing your ships to the front, especially in larger galaxies.

2) Only one ship per turn. Early on, the vision was that you could be funneling all your civ's production to a single shipyard and pump out a bunch of ships each turn. As it is, not only is that not possible, but if your shipyard has multiple sponsors, it is very easy to lose a ton of production each turn.

The result is that you are basically restricted to building one ship at a time near the planet that is sponsoring the shipyard. In terms of game-play, this is almost identical to terrestrial shipyards. The only advantages are that a few low manufacturing planets can team up on one shipyard and they don't take up a hex on your planet. On the down-side, they make it easy to shut down ship production, against which there is essentially no counter-play once it has happened. Mostly though, it just feels the same as before, which isn't horrible, but isn't exciting and interesting either.

Since I listed what I think the problems are, it's probably no surprise that what I think the solutions are:

1) lessen or eliminate range penalties. Either get rid of them entirely or cap them at some reasonable number, like 50%.

2) Allow for multiple ships to be produced per-turn. If you don't want to allow infinite ships/turn, what about logistics skill/5?