You can look at these types of questions from several angles: money, maintenance effort and quality of service.
Money-wise there is probably not that much of a difference, although it would not hurt to make the calculations for your usage scenario just to be sure.
In terms of maintenance-effort you are probably better of with using the Cloud SQL since most mundane tasks (such as creating back-ups and upgrading versions) are already handled for you.
Depending on your context, the quality of service of a 'hand-maintained' instance might be good enough, but if you need to support multiple sites then it quickly becomes a nuisance to create proper replications across the world (which from the looks of it is a standard feature of Cloud SQL).
Overall I would say it is greatly a matter of convenience.