I want ships to be used more in Destiny so bad. I like to ponder this idea frequently, and I was thinking if it was to be added I would really want it to have the same controls and point of view as that one mission in Halo Reach where you're defending the space station from a Covenant attack. Something Bungie could do to really set this addition apart from other ship flying games is they could make it feel different depending on whether you're in zero gravity or somewhere where there is gravity. I really like your idea for the PvE aspect of it though.
I like the idea, but I think a lot of those gear pieces should not be exotic. I think they should be more like strike specific loot drops, so on the legendary tier. I like the idea of having those drop activity specific loot though. Maybe not that much special stuff though, because that would make them one of the most easy to farm elements of the game.