Regarding random items: I've always thought of it as stuff left behind by trainers who are fleeing from Pokemon, given that the items tend to be near grassy areas or inside caves. I believe the explanation for why you lose money when you faint in a Pokemon battle is that you drop it as you try to escape, which would fit in well with this.
Regarding pokeballs "breaking": this is pretty easy to fit with my theory. If that idea is that pokeballs create mini-wormholes using a small charge of energy within every pokeball, then it could just be the case that any pokemon which escapes the wormhole uses up the entire charge, leaving the pokeball completely powerless and useless.
Regarding pokeballs not catching humans: I don't like the proposed solutions to this that involve intelligence. There are several dex entries suggesting that some pokemon are far more intelligent than humans (see: metagross). The explanation that "it's built to ignore human DNA" makes a bit of sense to me, but then you have to think...how easy would it be for unscrupulous people to override that? Still, that's probably the best explanation I can think of...none of the other ones make much sense.
Regarding trainers only being able to carry around 6 pokeballs: if my wormhole idea is true, it could simply be that occupiedpokeballs produce small amounts of radiation, associated with storing a pokemon in an alternate space. 6 pokeballs would be the highest you can go without reaching unsafe levels of radiation, while you can carry any number of unused pokeballs because they don't produce radiation until they are used to store pokemon.
Everything was beautiful. Nothing hurt.
I'm back, baby. Look for me in 5th gen UU!