I'm glad you posted this. I'm in a similar situation myself - three separate plots, each with its own MC, and I'm worried about the same issues. Wait - or is it five MCs? Or six? Oh crap...
It'd be much simpler, of course, to simply pick one of these plots and make it the primary focus, but I'm not ready to do that yet. Right now, if I'm putting it into my story, it's because I feel like it's important. Maybe this is pulling me in a dozen different directions, but I'd rather go to those places and then realize they were the wrong places to go, then cut them and risk losing something potentially powerful.
Perhaps when I'm revising I'll look at the work as a whole and realize what I thought were plots were actually sub-plots, or just fat. But - and maybe I'm wrong on this - in the meantime, I'm just going to keep my MCs, keep all my different storylines, until I get to the end of this and then step back and see what sort of animal I've made. The way I figure it, you never know what's going to happen in the process of writing the story - what will end up proving itself dispensable or indispensable.
Live fast and take chances, baby!
(and then revise like a bandit.)