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I have just completed a new implementation of 11g. So far, I'm content enough with the functionality and interface in 11g but, based solely on the difficulty of the 11g installation (EM was completely new to me though, so it may seem simpler for you) and the apparent ease of the 12c install (per the feature-set videos I'd viewed), I would definitely advise you to go with 12c if possible. Additionally, Oracle is making a concerted effort to steer folks to the 12c version so access to the necessary 11g files and docs is not as straightforward as it could be. Oracle has also indicated they will not be further developing the 11g version.
Potential reasons for why you might want to select one version over the other would include the type and version of the hosts and services that you want to monitor, what plugins you may need, and whether they're available for 12c yet. Our use of 11g was solely due to our need to monitor MSSQL and PeopleTools versions that were not supported on 12c at the time we implemented.
The certification matrix (on MOS) is going to be your best bet for determining which version you can/must use. If your environment and monitoring requirements allow you to use 12c, that would be my recommendation.
12c should be the default choice for any new implementation. There are enhancements across the board in Enterprise Manager 12c which include (but are not limited to) a broader set of features, a better UI, improved management of the EM environment (self-update, agent deployment, etc) and many performance/stability improvements. As Jeri mentions, 12c is also easier to install. Therefore, you should check certifications for the products you wish to manage using EM and as long as 12c is certified you should go with that. Also, be sure to install Release 2 of 12c.
Thank you Jeri and Mark for your replies.
Good information, good point about Oracle no longer making any enhancements to the 11g version. I was looking at the EM 11g version and it seems to be stuck at 11.1
A EM migration is a major undertaking for us, with 12C it would give us some longevity. Thanks again for your input.