Wow, those are some awesome ideas. I hope Heretic can get some of these implemented. Being able to fabricate medium/large consumables from the replicator would be awesome. Maybe white-> medium ground, green -> large ground, blue -> ship consumables, purple -> large ship consumables.
And the transporter idea is brilliant, another option would be % chance of boarding party shuttle to find new target if current target blows up, like a HYT does now.