I haven't started working on any pure Python (for App Engine) geometry predicates or operators, or any other alternatives to GEOS, but I've begun to make it possible. All GEOS dependency is being moved to its own shapely.geos module, which will be the default plugin provider for Shapely's new plugin framework.
The framework defines a few interfaces (geometry compiling or checking provider, area and length provider, bounds provider, etc) and entry points. When a geometry is asked to compute its bounds, for example, it delegates to a provider that has been wired up to the geometry factory on import. Here's a peek at how the default providers are registered in Shapely's setup.py:
setup(name = 'Shapely',
version = '1.1.0',
entry_points = """
And in shapely.geometry, the providers are activated with a function:
from geo import shape, asShape
from point import Point asPoint
from linestring import LineString, asLineString
from polygon import Polygon, asPolygon
from multipoint import MultiPoint, asMultiPoint
from multilinestring import MultiLineString, asMultiLineString
from multipolygon import MultiPolygon, asMultiPolygon
from collection import GeometryCollection
Users can override the default GEOS providers by writing and installing (with setuptools) new packages that provide the same named end points, and "using" those at run time:
from shapely import geometry
point = geometry.Point(0.0, 0.0)
x = point.buffer(10.0) # calls on provider defined by MyGeometry package
In theory, this makes it possible to a write an application using Shapely that can run on either C Python, Jython, or IronPython using the appropriate backend for the platform, as long as setuptools and pkg_resources work. I've read that they will in the next Jython release. IronPython seems to be a little farther behind. In practice, the plugin framework is helping to improve the testability and quality of Shapely's code.