TelsBoy:
I think your arguments in the main are more pertinent to hobbyist drone operators than those that would be operated by Amazon and similar large companies. You raise many good objections, but some of them are legal and can therefore be 'sorted' given sufficient clout, and in most senses drone deliveries would be less threatening to aviation than your average hobbyist.
If I had a drone, I'd want to take pictures from interesting places. I'd want to see how high it could go. I'd want to take pictures of big events like carnivals. That's what's cool. Whether I did any of these things would depend on my interest in the law and willingness to follow it.
The actual reason I don't have a drone is that I'm too law abiding to do these things, and instead I have a helicopter which is far more interesting to fly. Hardly anyone can fly r/c helicopters. In contrast drones are fly-by-wire. The aerodynamics is all abstracted out and you couldn't control one directly if you tried. Amazon needs a team of PhDs sitting in a room developing software to route the drones automatically, crash them gracefully and harmlessly should they fail, and once they've made them safe to lobby with governments for changes to legislation so that they can fly legally. If there is a person directly in the loop, they're likely to be limited to loading packages into them for the minimum wage. There's no reason for the end user to understand aerodynamics any more than my Mum understands an internal combustion engine. There'll be a team of PhDs in a building somewhere who are taking care of that side of things.
As for all the issue about IFR flight plans... Simply a non-issue for operations such as this. Provided you are low then there'd be no reason to follow all the rules set up for manned aircraft. Even in the middle of a cloud you can normally see 20 feet. An aircraft with GPS guidance that knows where it is, has a reaction time in milliseconds and can pull 5Gs is going to be able to operate in a very different way from a human pilot trying to read the map and fly by reference to an NDB.
Amazon wants to transport stuff from A to B and doesn't care about how it gets there. They would be quite happy if trained moles pulled packages through tunnels, so long as they did so reasonably fast for a reasonable fee. There's no reason to transport stuff at any significant altitude - you could have the drones follow roads at an altitude of 6" higher than the tallest double-decker bus and they would get the packages where they need to go. They would be less intrusive if they were ten or twenty metres higher than that, but I see no reason for them to fly high enough to pose a risk for aircraft provided they stayed outside the airfield boundary.
The only aircraft you could possibly need to worry about then, would be helicopters, and soon see-and-avoid technology will be mature enough that even they aren't an issue. I'd wager they will be agile and adept enough that you will be able to fly a manned aircraft through a cloud of drones and they will scatter around you like pigeons avoiding a peregrine. In fact, I'd wager someone will demonstrate this as a stunt within the next two decades and possibly much sooner.