Some new thoughts as I slowly crawl through the episodes....
1. The Initiative storyline wasn't nearly as bad as it is made out to be, it was just poorly implemented. The problem really was they threw every military/government stereotype in the book against the wall in the second half of the season trying to make something stick (and it didn't). They're inept! They're overly cynical! They don't know what they are doing! They're making it harder for regular people! They're aloof! Blah, blah, blah. It was very trite and could have been in done in more interesting ways.
2. Similarly, the Jasmine storyline was good except for the buildup. In the end, Jasmine made no sense given everything that preceeded it. So, she needed the Beast to murder a bunch of people in order to.. bring about mind controlled peace? Um, what? The idea of human will being a dualistic blessing/curse was very interesting... the execution of the idea... not so much.
3. Along those lines, the greatest failing from ME's writing was always their overall execution of storylines. For some reason, it seems like they give up on them about half way through and half ass them with deus ex machina or other contrived, non-sensical plot devices.
4. When you get right down to it, the characterization of both shows, as a whole, was odd at times. In one way or another, Season 6 of Buffy ruined every single of the characters in such a way as to make them all unlikeable.
5. Both Riley and Kate were interesting characters that were never really giving a chance by either the viewing audience or the writers to succeed. Specifically Kate, who's inexplicable blaming of Angel for her father's death ruined her character beyond what was necessary.