> I do understand that they are using a generic engine (Clutter) for this which can do lots of other fancy things that won't work as well without acceleration, but surely this sort of edge case could be detected somewhere in the stack and fall back and work nicely even without acceleration.
I don't think it's worth it for a forward looking project to care about stuff like that.
The GPU is part of modern PC architectures. Just as much as your processor, memory controller, Sata controller, and so on and so forth. For Gnome shell to take advantage of it to accomplish it's goals just means that they are writing efficient software.
For fall-backs you will need to use software rendering pretty much no matter what. It's still somewhat common to have real 2D acceleration and that was used for composition in the pre-mutter version of Metacity, but that is rapidly going the the way of the dodo. GPU is the only 'acceleration' that is available going forward and it's easier/better to use a standard API to take advantage of it.
Software rendering of OpenGL should technically be OK, but the Mesa software rasterizer is really shitty and gives extremely poor performance. the LLVMpipe-based software rendering should be sufficient (even getting games like Unreal Tournament 2004 playable on very fast processors), but the API not complete enough yet to support clutter.