Native commenting is still the way to go if you take the time to find good plugins to enhance it.
I'm really impressed with WpDiscuz. Couple it with Postmatic and you have an awesome comments template, ajax posting, livefyre-style updating, comment voting and email notification *with email replies*. With almost no overhead.

The two don't work out of the box together quite yet, but we've reached out to gVectors to make sure that happens. I did wire them up on my own tonight and it was amazing.

If you want to see a very bright future check out this demo. I promise you won't be disappointed.