From my experience (which is kind of a lot after I've built a standlone for my Vette), standalones are good for when you have a seriously modified motor, and/or you primarily race and don't really need to worry about a 'street car'.
Pros of a standalone are FULL control over everything
The con is that to get it as good as a factory tune, takes a LOT of work. I'm talking coast down, cold-start, part-throttle in varying conditions, etc. It's easy to toss it on a dyno and tune the A/F for WOT, but as they say, the devil is in the details.
The other con of a standalone is they rarely have as much basic functionality as the stock unit. What I mean is that an AEM or Motec most likely isn't going to throw a MIL light when your gas cap is loose. Forget about OBDII.
When you think about it - why do most people get a computer? Because they want to play with their engine tuning settings. What do they want to play with? Fuel delivery and spark - that's about it. Using a standalone for those adjustments is sort of like breaking out the sledgehammer to put in a finish nail.
Just MHO of course.