it's all about the math.
If you increase the stroke on the crank, the piston will push further upward, so you either:
A: get a shorter rod and shoot the rod/stroke ratio to shit
or
B: Move the wristpin in the piston upward, possibly causing oil management or compression issues.
It's really a tradeoff, but alot of companies are making some nice stroker kits now for B series cars that have a decent Rod/Stroke ratio, while they increase displacement .1-.2 liters.