There's going to be a 2.0 version of shapely. Joris Van den Bossche has written an RFC for a roadmap.
Joris is a Pandas and GeoPandas developer. The GeoPandas team has identified some enhancements to shapely that would allow GeoPandas and shapely to reach new levels of performance, and we're going to implement them. A NumFOCUS grant will support some of this work.
I'm super late in blogging about this and commenting on the RFC, which has lead to a little confusion about whether I'm in favor of this. I am, 100 percent. Rewrites aren't easy, but this effort has a lot going for it: serious use cases, committed stakeholders, clever and pragmatic programmers, funding, and lots of goodwill. We're going to have a 2.0 version that removes cruft, adds killer new features, and isn't super difficult to migrate to.
Please read the RFC pull request and comment if you're into helping shape the future of Python's #1 open source GIS geometry package.