Here we go, answering myself, before anyone else does :)

> Modularity, Namespaces and compatibility layers seem like the (only) way 
> forward

Change sets are an alternative, and the mechanism for them is already there.
But this does lead to the "many headed beast problem" :)

Or as mentioned prefixes, another simple solution.

> This approach would also give the structure for compatibility with 
> mainstream (and/or other dialects of) Smalltalk.

I would like to choose the dialect/libraries either squeaks, of Flow, or ...

> Probably a lot of work, although most likely worth it in the end.

Probably still worth it in the end, as modularity and namespaces would solve 
many compatibility problems neatly.

And this would tame the beast...

Aaron