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I've found OEM 12c to be a huge step up from 11g for Exadata management, particularly in terms of initial setup. If you've gone through the process in 11g, you'll know there are many plug-ins to deploy for full monitoring: InfiniBand switch, Cisco management switch, KVM switch, ILOM, PDU, etc. I've also found agent high-availability in 11g to be quite complex to configure.
12c on the other hand has the concept of an entire Exadata system, and can manage all the Exadata components centrally.
Also, in 12c we've started to see the capability to actually make configuration changes to storage servers rather than resorting to CellCLI; IORM for example now has a slick new interface for creating and managing resource plans.
I'd suggest prioritizing a 12c OEM upgrade to happen before your Exadata upgrade, so you can avoid the pain of an interim 11g OEM configuration, and having to change it soon after.
Excellent advice, Marc. Thank you. I hear what you're saying about the plug-ins - we've definitely had problems attempting to configure those.