I go with Crew -> Deck -> Rest of the ship. You can get the Crew faster than the ship upgrades so you can benefit from it a couple of voyages more. I usually go for the morale boosts (ship upgrades) before the others (Sirens give Seafaring + Combat and Golems give Combat + Morale so I usually lack morale when I combine those 2 units)
If you do the story voyage you won't be able to do the chimes/gunpowder one and vice versa. As far as I am aware if you do the biologist voyage nothing will happen to the missionary's voyage.
To get a better crew you need gunpowder. To get gunpowder you need to run the Skulls. Even a 10th leveled crew Brimhaven pirate (for example) will have only 300 combat, while a lv0 Eastern Musketeer will have 350.
can't you just pay the black market jagex employee to fix it up?..... inb4 you need to start paying with runecoins It is an option ... and I did it, but it's really illogical to have to fix a ship in order to use the crew.
The only thing I dislike is that if your ship needs repairing you can't use the crew/captain of the said ship ... so if you've sent you're best crew on a mission which failed you pretty much HAVE TO repair it =/
As someone above me said - they (and I assume everyone with nex armor or any nex hunter actually) want the armor to be rare. Unlimited voyages wont help with that.
I can't shake the feeling that PoP looks like a facebook game (farmville for example) and still ... I was more happy to find a 160/200/140/100 captain than having a good drop ingame xD