Reiterating what OP said, we no longer need shards or energies to upgrade our stuff. But now, gear / weapons serve the same purpose. We use them to make our current gear more powerful. If that makes any sense. Also, even shards and energies had a good use later on. You could exchange them for motes and buy exotic engrams off Xur. Just because something has always been bad doesn't mean you should leave it that way.