Currently, to output web files to show clients, I render out a loseless animation .mov from After Effects, then bring that into compressor. And then output an h264 streaming .mov usually at about 1200kbps..
Is there a way to eliminate a step and get the same result directly from AE?
Due to the nature of compression and the nature of Rendering, you won't get superior compression without compressing a pre-rendered movie. Compression schemes look to the frames before, and after the current frame to compress the data more efficiently. You can generate a .h264 movie out of AE, but the render engine won't be able to process the frame "after" the current frame, as it hasn't been rendered yet, and as such, won't be able to provide the best possible compression. Your current workflow is more ideal, although it is an extra step.