You guys are forgetting one very important part of the puzzle. I have seen and experienced supposed professional tunes that ran worse than a generic map. The trick is finding a truly capable tuner. Anyone can be a "professional" tuner; all the word professional means is that they get paid to do what they do, whether they're worth a chit or not. Kind of like that millionaire outfielder in baseball who bats .159 and drops half the fly balls hit in his direction.
If someone has a known good tuner available to them, then by all means take advantage of a custom tune. But for those who are stuck with the idiot nephew of the local dealer as the only local tuning choice, a generic map from a reputable guy like Steve at Fullsac is liable to be a better choice. Tweak it with some V-tunes and you will be better off than most. And let's face it, if the bike runs well, most of us would be more than satisfied even if there was another couple horsepower we didn't get. Most of the folks asking these questions aren't involved in major builds or racing, they just want a better running street bike. If you race it or run dyno shootouts, then yes it makes sense to spend a bunch on tuning to get that last tenth of a ft-lb. For the rest of us, not really.
Jerry