Yes, the mandatory quests suck! I once was allied with one race and at war with the other. What did the guild do? it gave me the mandatory quest to protect the race that I -and the guild too(!)- was at war with! What the feck? It`s like Obama tells his troops to protect Al Kaeda!
I changed the guild involvement to "minimal" and I didn`t have any mandatory quests yet again. So it seems as if this option turns of mandatory quests completely, which is good!
I first found the crew thing weird, too. But then imagine to be a NASA Engineer: Everything you have on your ship -weapons, thrusters, hull or crew- has a mass (weight). The more mass on a ship, the more fuel is needed to transport them. Crew members also need food, water and other things, which have mass, too. So it`s not that unlogical as it first looks!
The monster spawning is normal for Diablo like games. You need monsters to get xp, money and equipment. No such game does really explain how monsters can respawn. Maybe in this game monsters are hatched in outer dimensional pockets, who knows?
For the races there are spawning points. Planets which produce Spaceships. Destroy them and no ships will respawn!