Different remotes and different remote protocols isn't the problem with consumer electronics. The lack of an additional standardized communication protocol is what's missing. Something that would let the components communicate with each other wired or wirelessly. A number of efforts have come and gone of the years and a few are still around, though with no signs of gaining significant traction.

The computer software analogy isn't the most appropriate one because the interaction involves a manual targeting operation - choosing which application will be in focus to receive commands. One of the main goals of a good universal remote is removing the manual targeting/selection of components and that's where one of the biggest challenges comes in this product segment.