it's a lot easier to tune a standalone than it is to tune the stock pcm, esp for the average person. It's also usually easier to find a decent tuner for an aftermarket system than it is to find someone good with stock pcms, for the same reason.
To tune your own pcm, you're looking at probably $500 to get started, maybe more (gotta buy a wideband, gotta buy an interface for whatever software you're planning on using, usually you've gotta buy licenses at that point). Everyone says "just tune the stock computer" but if you've never messed with one before, the learning curve is quite steep, much much more so than most aftermarket systems.