One of the things I always disliked about the original Digg was their threading. The slashdot like feed where the oldest comments were at the top and there was only one level of replies tended to encourage the "first" comments and harmed the quality of the discussion. I was glad to see it use a reddit-like comment thread for the new site, but it also meant there wasn't much reason to use it over reddit.
I'm a bit surprised with Alexis' involvement they didn't anticipate the bot problem. Alexis left reddit several years ago but I'm sure he's still in touch with the folks who run the place. It would've been worth it to talk to them about the threats they currently face and how they deal with them.