>Any ideas are welcomed and appreciated.

I'm using PureMVC [1] AS3 multicore [2] to separate my apps into
independents modules or cores.
The PureMVC cores communicates using interfaces [3] or the PureMVC pipes
utility [4].
With this approach you're able to implement encapsulated and reusable
modules that holds your business logic which doesn't need to know anything
about its views. You could create and remove PureMVC cores at runtime. If
you take care of implementing your PureMVC cores using pure AS3 you could
just reuse it with FlexJS.

One word to PureMVC:
PureMVC consist only of a couple of files, it doesn't generates a dependency
like other big frameworks does.
It's matured, unchanged over years (which is a big benefit!) and still
supported by its owner Cliff Hall.
There're exist ports to lots of other popular languages so that you even
have a fair chance to port your buisness logic to any other language.

HTH,
Olaf


[1] http://puremvc.org/
[2] https://github.com/PureMVC/puremvc-as3-multicore-framework/wiki
[3] https://github.com/PureMVC/puremvc-as3-demo-flex-modularity/wiki
[4] https://github.com/PureMVC/puremvc-as3-demo-flex-pipeworks/wiki



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