Robert, Most of these annoyances have been talked about on the Eagle chat forum
I know you can do this as well as take an existing schematic and PCB and export a complete library with the parts in your sch and pcb files. It's been a while since I have done what you are trying to do but I believe I have done it. I suggest checking out that forum. It's a great resource.
I've been using Eagle for the last 12 years and had to change over after using PADS for many years. Over the last 5 to 10 years, Eagle has gotten a lot better and even though PADS does a lot of things better than Eagle, I still prefer eagle mainly because of the user base and the online help that PADS never had. Also, the price is good and I don't have to pay Mentor Graphics thousands of dollars of ransom money just to ask a question every year.
You can even suggest changes to Cadsoft that might be incorporated in a future version. They do seem to listen to their customers. boB