I have to show this off... AJAX Inline Comments
So, my solution was to use AJAX to download the comments as needed. That is, when you click "show comments here," it downloads just the comments you wanted to see.
Also, I used Moo.fx effects to fade and "slide" them in and out. Let me know what you think.
NO, I CANNOT make this into a plugin. It simply requires too much theme editing. Of course, if you wanted to hire me to do it on your blog, I'd be happy to oblige. :-)