I would agree that Jonathan's "tragic flaw" is his tendancy to take the easy way out and not work to solve things. Which is why I find what he says to Buffy in "Superstar" about her relationship with Riley taking work, so ironic. The poor guy can't even take his own advice!
but, I would argue that the Trio aren't even the primary villians for Season 6. In my opinion, they're a distraction, a device Joss uses to keep our attention off of the real menace that's building, and then Warren (with his oh-so-manly gun) becomes the device that releases that menace. Willow's magic "addiction" (and it's consequences, like bringing Buffy back from the dead) is the real issue that's building from the first few minutes of Bargaining pt. 1 on. And, if you think about it, Willow has the same flaw as Jonathan. She looks for the easy way out, and for her, that's almost always magic. (Exhibit A: The extra-biodegradeabley party decorations, the "I will it so" spell from Something Blue, dressing in 3 seconds with magic, etc etc etc.)
Ok, to get back on topic, I love the Trio, because I am also a sci-fi/fantasy nerd (and proud of it!) and I relate to them...when they're not being all evil. I loved Adam Busch, because he made Warren just the creepiest guy on the planet, even when he's just building a creepy AprilBot. Danny Strong is just the cutest thing and Tom Lenk is obviously a great comedien. But as far as the characters go, I was rooting for SOMEONE (not Willow, cause of the consequences) to kill Warren by the time Dead Things rolled around.