The "proprietary aspects" of a tiny stepper driven extruder are less than trivial to the company that created the first mass market laser printer. You can't fight gorillas with gorilla-ness when you're lemur sized.

The primary asset Makerbot has is the community. Its fine to polish the product to make it more useful to those less skilled, but lock the community out of the product by closing up the software and its over. That is exactly the advantage someone like HP needs. Theirs is going to be just as good or better eventually with or without Makerbot's suuuper secrets. In the end, the only differentiator will be community.