>>38361437It's really not that complex. For nature's, each one boosts one stat and decreases another. Pic related is the relationships for each nature. The neutral ones literally boost a stat and then decrease that same stat.
With the physical special split, before generation 4, physical and special attacks were determined by the Pokemon's type rather than the move itself. This got pretty silly because moves like Bite and Crunch we're special attacks because Dark was a special type, and shadow ball was physical because Ghost was physical.
Gen 4 introduced the split so that what the move actually did determined whether it was a physical or special attack.