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• Community over code: MyFaces community counts with a lot of folks with outstanding knowledge on JSF. Suscribe to user and dev mailing lists are the best way to know what's going on, receive feedback and know other people interested in JSF. This is an important consideration, because sometimes you can find a bug or need to ask something to somebody about JSF.
• Innovation happens on MyFaces: MyFaces is not just a JSF implementation, it host other projects (Trinidad,Tobago, Tomahawk, ExtVal, CODI, Orchestra, PortletBridge RI, ....) that provides additional functionality not provided by JSF implementation itself. Many of these projects are compatible with both MyFaces and Mojarra, but you should note that those projects helps MyFaces Core to keep code in good shape, because all those projects test against MyFaces Core, and if there is a bug, it is handled more quickly (because everything is handled "in home").
• MyFaces Core generates code using myfaces-builder-plugin: these project is a maven plugin that with myfaces-builder-annotations provides a jsf development kit to create multiple artifacts (components, converters, validators, client behaviors) and handle all documentation related in an easier way, minimizing the number of files you need to handle. It uses java annotations to feed all related information, and each myfaces jar using this tool has a myfaces-metadata.xml which contains all meta-information required to build each bundle. This tool can read composite component definitions and build an integrated documentation with your normal components, converters or validators.
• MyFaces uses Maven, so edit the code or rebuild it is as simple as open any maven project with your IDE. Note that most IDEs has built-in support for maven.
• MyFaces Core is "OSGi" friendly: It provides some SPI interfaces to deal with special setups, when you need core control over classloading. A lot of good stuff has been put in this area.
• MyFaces Core is tested everyday against MyFaces UI component libraries and Add-ons/Extensions. If a bug is found, it is solved quickly because it Many of these projects are compatible with both MyFaces and Mojarra (because they are build on top of JSF standard), but you should note that those projects helps MyFaces Core to keep code in good shape, because all those projects test against MyFaces Core, and if there is a bug, it is handled more quickly (because everything is handled "in home").

For more technical reasons why choose MyFaces core take a look at this blog.

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