Thats exactly the kind of thing that is adressed - basically the only regions that can be invaded are the ones with a port sea region - also the AI factions should be better protected if the total number of sea regions is small. You are right in that it is a compromise and that taking out ships altogether is the best thing - the only problem that i see with that is that some gameplay and some flavor is taken out completely. In paper that might be inconsequential - yet perhaps when implemented it might turn out too dry.
EDIT
I wouldnt mind to take out ships altogether at all - and put on weight in other things like faction rosters, strategic imoprtance of tech trees in relation to recruitment and unit stats.
!it burnsus!
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