Most good turn-based 4X games automatically develop your cities or colonies or whatever you're dealing with. I'm not as familiar with GalCiv as I am with the more land-based Civ, but I know that in the latter game research is done automatically and city improvements are worked on every turn. Perhaps to make Sins a bit easier to manage, this could be implemented in some manner.

For example, in Civilization, a popup window appears whenever research is complete asking what technology you'd like to work on next. Now, with Sins, this is impractical, as it's real time. However, if a research station is free, the research button could begin to flash. Once clicked, a specific technology could begin flashing as a "suggested" technology, much like how Civ 4 (or GalCiv, I'm not sure, haven't played it much) suggests technologies. While not automatic (as this would give you a case of, "Hey, where are my credits running off to?"), it does give the player some more prompting to keep research moving. Sometimes the "Research Complete" announcement isn't noticeable in the heat of...something else.

As for planetary modules, I'm personally not sure of how a similar system could work. While this thread is open, try your ideas for this.