Rapture's Immigration Staging :
Considering that the bulk of ~ 40000 people came to Rapture in the space of 4 years (about 200 per week), there must have been staging areas for that transportation -- for not just the people, but their possessions and commercial inventories/stockpiles. The logistics of having people showing up in small numbers from many tiny boats would be rediculous (and hazardous). Instead many would have come in regular shipments via converted freighters and passenger ships, with all their possessions prepacked to be taken down below to Port of Rapture.
Rapture's location is about 2300 miles from New York City, which would take about 5 days one way at a typical fast freighter speed (straight running, assuming no delays). The actual origination points might be much further away (the Novel mentions one - for construction materials coming from NYC), and again the weather/port scheduling might not always cooperate.
The facilities at the Lighthouse would be substantial, to be able to transship such quantities in a safe and timely fashion. Remote staging areas would have to have all the needed ship docking/loading/servicing installations and there would be the small fleet of ships themselves, shuttling between the various staging locations and Rapture (usually many thousands of miles per trip). Ryan's industrial empire could supply some 'abandoned' industrial complexes to be put to such purposes (as transfer points, as the people converged from across the World). All of this huge operation would be greatly complicated by its secretive nature and the round-about paths people would be made to take.
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Lighthouse Entryway :
Thinking about the Welcome Center Bathysphere Station (where the Player disembarks from the trip down from the Lighthouse) :
- Why is the Bathysphere from the Lighthouse still operating - except for Ryan's men who should be the only ones allowed ?
- Why is there that Bathysphere waiting on the surface (at the Lighthouse) ? Wouldn't it have been a little smarter to NOT have one ready there to take anyone who stumbles on the place down to Rapture automaticly? ( Atlas arranged that ??? ... When Ryan controls the system and allegedly there is a genetic lock blocking such manipulations ??? The 'genetic lock' thing becomes much more dubious...)
- Why isn't there a security checkpoint there in the Welcome Center Station, as the most obvious way someone could get into Rapture (or out). There are no Security Turrets (working or wrecked ones) to be seen. No Security Camera aimed right at the docking port (we certainly see enough such security still around Rapture). -- Even just to keep the Splicers/Atlas's thugs away from such an important transportation infrastructure.
- Why are those big doors/hatches (the ones you see there in the Station that would cover the holes the 'Bathyspheres' rise and descend thru) NOT closed and locked ? They should be sealed just for safety (Why risk a failure flooding the entire area ? - it is simply common sense).
- Why is the Lighthouse even still there? You could at least have turned off that big light. If it is still used for some shipments from the Surface that late (1960), at least shave it down to make it less obvious and turn on the light only when it is required.
The Lighthouse Bathysphere should only go to Welcome Center as a special path -- instead of to any other place. That would explain why we get no destination selection on its Control Stand. That would be an example of an obvious/simple security measure.
Simple answer to all this is : With any obvious security measures in place, the games plot wouldn't have happened. Ryan wasn't that stupid, but the designers assume we will buy such illogic.