So part of the PVE experience is to meet new players around the ATLAS and ally with some of them that you like to run PVE things with.
So on that note some thought on this:
1) make alliances unlimited in PVE
2) Make a way for alliance members to be able to build a bed on another alliance boat
3) Make cannons, sails, repair be able to be performed by an alliance member
These changes would GREATLY boost the experience of PVP play in Atlas