I've decided to switch back to Disqus for commenting. I tried it out a few years ago, and had quite a few problems with it, but as time has gone by, I've noticed that a lot of the issues I had, are no longer happening for other bloggers.
The biggest reason I'm switching back is that it does make it easier to reply to every comment. I try to respond by email now, but with so many people not setting up their email address for Blogger, it's becoming a less frequent option for me. I'm going to miss having the comments pull up in a separate window, as I do think that makes it easier, but I'll learn to live without it.
Hopefully this transition will go smoother for me, than it did a few years ago. I'm going to keep my fingers crossed.