Simulink now has the feature of Reconfigurable Subsystems. These are parameterizable library links - that is links that conditionally reference different implementations. I put together a simple example of this with a very simple filter optionally implemented with single connections, or using vectors.
The Library File:CondLibTest.mdl contains the implementation and the Reconfigurable subsystem 'switch'. The Model File File:Foo.mdl is just the test model into which this library block has been embedded. Here the simple parameter just switches between implementations - but obviously far more complex decisions and alternate implementations could be done.