Regarding #3 I think they want the patent holder to prove he is actually using the invention for a (commercial) benefit. If you invent a copy protection scheme they want to see you actively sell it to third parties or actively use it in your own product.
I think that makes sense to be honest, people shouldn't be able to sleep on an invention until they find a suitable company to sue for high profit margins.
Edit: This is in reply to points about software patents only.
Isn't it rather possible that the right answer for software is not like the right answer for drugs, and that it takes an expert in a particular field to propose a sensible reform (assuming one is needed in that field)?
#3 sounds good, but how do you stop people from submitting code written in Brainfuck or TECO or something?