The Ship Graveyard has tons of quest-only caves that are on their own map layers. Since you can't re-visit them, it only makes sense. However, all the revisitable caves (basically those with all the bosses) are also on these separate layers that can't be accessed from the overworld map, making it unnecessarily difficult to track party members.
In other words:
Move the following caves to the map's sub-level 1:
Sea Tramps' Sanctuary (both west and east)
Seagull & Pelican Island Caves
The three caves where Levadis, Inker and Admiral reside