The engine is tuned as stock to achieve optimum mix of a few things, such as the MPG, engine life, engine emissions etc... As well as also to build a range of products
The down side to a remap is the loss of warranty, dealer support should something drastic go wrong, and an increase in insurance premium, and sometimes a devaluation come resale on tuned cars, as they are perceived as been trashed/tracked.
Obviously these points don't put everyone off, and many tune and lead happy lives, but not everyone is so lucky. I chipped my last car, and from those experiences I did it the more expensive way this time with the JCW conversion.
Each to their own, many will say a remap is the cheaper route to more fun, but thats just looking at the price of the remap, not any of the other potential costs you could incurr.