Another simple enhnacement idea, for Manufacturing this time: adding maxEngineers setting to an item manufacture project. It would disallow to throw more Engineers at an item than this setting allows (like Stanisław Lem said, making fun of what he called 'military logic': the fact that a single person needs 200 minutes to dig a hole, doesn't mean that throwing 100 people at this job will result in the hole being dug in 2 minutes; a more likely result is people killing each other with shovels).
Same might be done for research (maxScientists; Lem was talking specifically about research, after all, and using physical work just as an example) - not that important in Piratez, as your number of Scientists is limited any ways, but would be immensely useful for vanilla-enhancement mods, like FMP or X-Ops or Hardmode.