Haha yeah, I definitely feel your pain - as a caffe developer it really makes me cry when things get so incompatible. I've made some improvements in caffe2 to make it more modular - checkout http://GitHub.com/caffe2/caffe2_bhtsne/, things like such will potentially make things more maintainable than the old Caffe solution.

I think Caffe 1.0 made a fundamentally flawed design choice in using protocol buffers to represent network without allowing users to provide a standardized way of adding new operations. Since network was represented as protobuf, to add new layers you had to recompile entire library or use python layers. Thus as a result each project had a new Caffe fork which had to be compiled and maintained separately. Caffe 1.0 was ahead of its time in several aspects compared to Theano or Torch but the dependency hell combined with per paper fork made it difficult to use. It should be case study in unintended consequences of design choices.