Yes, though no definite decision yet. My current thinking is that I will
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Add some way for marks to have more control over which marks they can coexist with (to allow multiple instances of a given mark type at a single spot, or forbid certain marks from occurring together) to address some simple use cases.
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Require that inline nodes with content are rendered with a custom node view, as a way to put the responsibility of hacking something together that happens to work for a given use case toward the client code. So if you want a nested structured node in your inline content, sure, but you have to kludge together the editing interface
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Make it easier to use nested ProseMirror instances in custom node views (primarily by providing a way to map steps in a given local node that is the top level node of the nested editor to steps in a wider document)
This isn’t going to solve everything, but I think solving everything may be out of reach, and it’d already be great to have a working approach for these kinds of situations.
Doesn’t a tree-based representation suffer from similar issues? Unless your link mark is the lowest-precedence mark in your schema, it risks being split by other, lower-precedence marks.