@AlanHK...
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However, simply deleting lower level headings in the TOC is not good. If it doesn't combine them it should leave them. Now it erases all subheads within a chapter.
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Deleting what from where? Deleting subheads from the NCX TOC or deleting subheads from within the xhtml files? I tested the plugin with a test file which used h1, h2 plus a third heading(formatted with h3) and there were no problems or deletions in the NCX or epub html. I also tested my plugin using a much larger and more complicated epub file that also used 3 heading levels -- including subheadings. The plugin didn't have a problem with either test file and there were no subheading deletions. Of course if you don't format the appropriate headings using just h1 and h2 styling then you will probably get problems. But that's all explained in the plugin release notes which I'm sure you've read already.
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And configurable separator character would be nice.
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When you say configurable separator character do you mean being able to configure different font characters/symbols with different font sizes etc? That's not really necessary since you can easily reconfigure/restyle those separator characters manually anyway after you run the plugin. I always prefer to keep plugins simple -- and if you want to do something more exotic you can usually achieve those changes manually in the CSS or you can do it using grep S&R.