Water based puts what I like to call a "thin candy shell" on the surface. It looks great at first, but ultimately starts to scratch, chip and peel away from the surface; normally requiring a strip (which is difficult with acrylics) and restain. Since it doesn't really penetrate, it also doesn't give the wood fibers the moisture it needs, which leads to splitting, cracking and warping.
On the other hand, a true oil based stain (I prefer A/C brand) pentrates deep into the surface, bonding with the fibers of the wood. This prevents that scratching, chipping and peeling. The oil also conditions the wood, keeping that needed moisture there to avoid splitting and cracking. It can even help seal up cracks that have already happened due to lack of moisture. And when it comes time to re-stain it, it just requires a simple wash before staining (providing you are applying the same color stain...and obviously those two steps aren't done same day).