Going for bukkit is a good move, yeah.
As for the chunk loader blocks, i don't see them as indispensable, except for mass fabricator setups like you mentioned.
Now for teleport pipes...I'd be against removing them. They're one of the only things that makes having remote quarries/oil rigs practical. Let's just say that placing a pipeline and a cable line for hundreds of blocks isn't practical at all, especially when I have to move the quarry when it finishes. With the teleport pipes i only need one pair to handle power, and one pair to handle item 'porting back to base. The same thing can be said for an oil rig (pump and refinery). One thing I want to know though, what is the radius (with center on the player) for chunks to be loaded in multiplayer?
Nether ores can go. They're not that really useful, what with the EXPLODE! thing and Pig Zombies going aggro through proximity. Yeah, they can sense you have ore through walls.
For the permission things, I'd say that would be cool. We just have to be careful so a guest won't be able to come in and abuse some sort of exploit to grief. The lockette plugin for bukkit comes to mind. When I played on a server that had it, people were able to abuse it and get inside other people's chests.
For the economy: I'd say go for it. Though I wouldn't participate much.