I can tell its been a long time since you played. Crew from planets was cut in favor of streamlined rules. You just build and go now. They figured that since you must have a supporting population medium size or larger to build ships the crew you need will be there already.
SE5 Crew and Control are set by me. Take a look at SJ's GGMod. He has a very complex crew system. As for the crew/planet portion of your question I don't know of anyway to tie the two together outside of the fact you need to build facilities. Limiting the crew points to only the system they are produced in is not possible. SE5 will not restrict the ability the SpacePort uses. In other words I can't tell it to ship only organics and MCs but not personnel. In this case I won't need to rely on handwaveum to explain what is going on. This is an interstellar empire so populations and crews are going to be shipped about. Not by canon but if I was going by canon I would have to restrict the ShipYard Component to only planets with certain populations. That won't happen!
My ideas for a facility are "University" which produces trained personnel for crews. I was also thinking of "Military Academy" which would have half the production of the University, cost twice as much, but provide the training ability in conjunction to the resource production. I am thinking of taking out all the production ability though, with the conversion to MC land is no longer in shortage. If I can ever get this planet generation sorted that will change the land surplus some. But I still need to get the right ratios of available space to planet size sorted out.
Re: Bugs ?
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