There are many differences between Hype and apps like Flash and After Effects. Being a major AE user, I appreciate your concerns. The ability to define start and end times for objects, to control loading arbitrarily and by object, the selecting of objects, etc.
As noted by Jim, small companies don’t have the resources and manpower to cover all requests, but must prioritize.
From my perspective, the issues are that Hype is the best app of its kind, that Flash (which has a ton of negatives) doesn’t run on iOS, that video apps such as AE don’t have the needed interactivity and require dedicated streaming, and that JS on its own is too complex for highly complicated animations. There are other issues as well, but for what it does, Hype is the best thing going.
Rick mentioned Photoshop 2.5. I started with 2.1. In those days PS did not have layers, which meant that complex compositions required the creation of all sorts of files that had to be output, then assembled while making multiple saves of slightly different versions and doing the same over and over for each layer - it was ridiculously labor-intensive. But that was the state of Photoshop. If the job required PS, then PS was what we used. As for Hype, stick with it. It’s the best app of its kind.
Regarding your point #6, if you export the project as video you can use QuickTime 7 Pro to extract the audio track. Open the movie in QTP7, go to Movie Properties, delete the video and timing tracks, then export it in the desired audio format.