I think the Pokeball system as is works. Correct me if I'm wrong, but there are only two kinds of usable items in Pokemon:
1. Items that get used up after 1 use.
2. Items that never get used up (Like Flutes)
It's a simple system and easy to understand. I feel that generally people don't say "Ugh, why can't I just use my one Pokeball over and over" rather than "oh man, I should have bought more Pokeballs before I went into the Seafoam Islands." It's just an unnecessary silver platter.