The stuck ships are a bug. Check again in a turn or so and see if you can move them then, or reload to a previous save and see if they move. If that doesn’t fix it you may have to kill off the ships or restart the campaign.
As to regions and buildings...Large regions have more options for buildings than smaller ones. Some of the choices seem a little subjective on the part of the developers, but that is how it is. The lesser regions only build a government building and walls. The greater region have the barracks, arsenal, maybe the admiralty, and so on. It can’t be changed and they never grow into a more developed region.
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