I'm not Jim, but...
1a. The scrolling can be turned off by pressing P. Jim is adding an undocumented feature to stop the scrolling.
1b. The old lighting cycle is impossible as the lighting in the old program was actual lights. The new lighting is largely based on shaders. I'm sure Jim is going to make some more improvements. Specifically I know he wants to provide a full range of colors beyond the current blue-to-green.
4. The interface was developed by Jim. He doesn't like spending any more time on the interface than he has to. He prefers working on the artwork.
Still, I do miss what we had before (not the fish picker so much, but the overall settings panel).
5. Hmm. The load time varies a lot. On the HTPC we built for our new HDTV, the MA3 logo barely comes up before it fades into the Aquarium. Have to say MA3 looks awesome at 65".