Asymptotic, I wholeheartedly agree with you in raising the overall "mineable" materials prices, so it wouldn't affect trading, but would make mining something of a viable activity. I can't see any problem with that, you just would need to make a study as to what sort of changes it would take so it would become an option, not a replacement to trading. Actually, I think trading should still be slightly more profitable, so people would still move around more.
As for missions, I too agree. There should be high level missions available at the Core systems. Not sure how easy or difficult it is to implement and what sort of balance issues could rise from that. If the level of the ships is determined within the mission's parameters it shouldn't be a problem, if it's determined by the overall level of the NPCs in the area, then I fear it may not come to terms (we can't have the same level of NPCs you find in the Border Worlds in New York, for example).
All in all, I say you have a good point here. Perhaps you should work on studying these matters and then making an official proposal at the correct forums after you've done so. I, for myself, would like to see something like this implemented if possible.