BuddyPress.org

I do not understand why people have these problems. BuddyPress has similar features as Facebook and Twitter and both those services have millions of users.

You said:
1 The concept of Forums being tied to Groups (no one “gets” this)
2 The serious disconnect between commenting on a blog post or forum topic in the feed vs. in the original
3 @mentions (99% of users are like… WTH is that?)

1 Groups in BuddyPress are like Facebook fan pages and yes Facebook fan pages have forums.
2 You can turn it off in the admin and force users to comment on the original post and not activity
3 @mentions are the basis of Twitter with millions of users who have no difficulty using the service. Also Facebook uses @mentions when you post status updates. You type @ then there name and they get notified about the message.

One last thing, BuddyPress is not really an out-of-the-box software. You should figure out what functions you want for your users and then use those. Having everything can be too much.