Soul mates AU where John and Sherlock did meet when they were kids, but didn't like each other (mainly Sherlock being a prat?) and their parents really didn't either. Later, Sherlock just decided soul mates were overrated and didn't want to meet John again. Until they meet by accident when they were older, and Sherlock now regrets not being interested in young!John. Up to you whether John recognizes him as his soul mate.
Unlucky soul-mates
Would also be fine with a Mystrade fill :D