In my experience, with large data sets (I'd say > 100 GB), you want to run your own database instances, if only so you have control over the small fiddly bits you need control over.
RDS: 1) Uses drbd for master failover (this introduces network overhead on disk writes), 2) Only gives you access to super commands through stored procedures, and 3) doesn't let you tune InnoDB to your dataset or performance requirements.
In my experience, with large data sets (I'd say > 100 GB), you want to run your own database instances, if only so you have control over the small fiddly bits you need control over.
RDS: 1) Uses drbd for master failover (this introduces network overhead on disk writes), 2) Only gives you access to super commands through stored procedures, and 3) doesn't let you tune InnoDB to your dataset or performance requirements.