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When deciding between Amazon RDS, Amazon RDS Custom, and Amazon EC2 for your SQL Server migration, you should consider the features you need, the level of control and responsibility you want, and the costs involved. Licensing is a big part of your decision to go with RDS or EC2. Only with EC2 can you bring your own license for SQL Sever with SA which can drastically reduce the cost. You can use license included on EC2 or RDS. Here is a rundown of the features you've mentioned and how they may affect your decision:
Full-Text Search: Amazon RDS for SQL Server supports Full-Text Search. So, you can use either RDS or EC2 for this feature.
Service Broker: Service Broker is supported for Amazon RDS, but Service Broker endpoints aren't supported on Amazon RDS. But RDS custom and EC2 support this feature.
SQL Server Agent Jobs: Amazon RDS for SQL Server supports SQL Server Agent Jobs. So, you can choose either RDS or EC2.
Linked Servers: Amazon RDS for SQL Server supports creating linked servers to other Amazon RDS DB instances running SQL Server. For linked servers to other database systems like Oracle, you need EC2 or RDS Custom .
Alerts: You may use Amazon CloudWatch with RDS for receiving alerts. EC2 and RSD Custom gives you more control over custom alerts.
Data Compression: Amazon RDS for SQL Server supports data compression. You can use either RDS or EC2.
DB Mail Configurations: RDS supports Database Mail for all SQL Server versions on the Web, Standard, and Enterprise Editions. You can use either RDS or EC2.
High Availability: Cluster and Always On: Amazon RDS for SQL Server does not support SQL Server Always On Availability Groups or Failover Cluster Instances. Amazon RDS provides high availability using a Multi-AZ deployment, which might be sufficient for your needs. If you need Always On or Clustering specifically, you would have to use EC2.
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Thanks for inputs/suggestions.