i have decided to start the game on multiplayer because there are so many choices for characters and everytime i find a cool weapon i need to make a character that can use it. What i was wondering is am i missing out on any of the story by playing multi i have reserved 2 spots for npc's

Only the reality that with more NPCs you access more storyline faster because each NPC has there own tale to tell and there own adventure in the process. (Well almost all)
Having only two means either limiting yourself to two, or accessing them slowly.