I get the feeling that Apostate, Gloomweaver, and the Ennead are a little too weak to be considered 2, 3, and 3 respectively. I think each one ought to be reduced a difficulty level. By contrast, I think basic Baron Blade might deserve to be a 2, but maybe not. What do you guys think, and are there any other villians that you think should be higher or lower on the difficulty scale?
A lot of it varies by whether they are on normal or advanced, and by what cards they get.
The Ennead on normal tend to be easy unless they get some more members out quick.
On Advanced they are one of the hardest villains in the game.
Gloomweaver has issues more than anything else, he just doesn't flip enough. When he does flip he's wicked.
I've never seen Gloomweaver flip.
With the Ennead the hero and villain mix make a difference too. Shu being immune to two types of damage can stymie small hero teams.
That's why you play Gloomy on advanced…oh, wait, nevermind.
And it has been discussed that size of hero team affects "difficulty" of various villains. The Dreamer is easier with smaller teams, but La Capitan or The Matriarch is easier with larger teams.
And then there are individual heroes that "own" certain villains, and vice-versa. Especially heroes with deck control powers keeping particularly nasty cards from getting played.
I think assigning a numerical, 1-4 rating to any villain, given the boggling number of interactions with hero and environment decks, is inherently flawed and will only be useful as a rough guideline.
That said, I agree Gloomweaver is a wuss.
Another thing to consider is for whom the difficulty ratings in the rule book are primarily intended.
Are they intended for expert players of the game who know the ins and outs of each hero, villain, and environment?
Or are they intended for brand new players?
Wait, are you saying that Apostate is too easy?
That's one I haven't heard before.
Apostate is the epitome of a 2 to me, in the sense that he can be really dangerous but isn't consistent. Sometimes he'll get the redirection combo of doom out and wipe you out and other times you just tank his damage to the highest and take him out pretty easily.
Compared to 3's like Voss, Dreamer or the Ennead who's decks have more sources of damage/denial and are therefore more consistent.
Gloomy is a 2 and Ambuscade is probably a 1, those are the only 2 that feel off to me
Well yeah. I've only played him once, so maybe that's part of it, but he really didn't seem to pose any threat at all. Lowest base HP of any villian (Other than the Dreamer who doesn't count, and Blade who also doesn't count because he gets a bonus 30 HP, and the Vengenance Villians who don't count), he never flips if you fight him intelligently, all you really have to do is whack his relics and demons, then kill him before he kills you (and even if you lose a hero along the way, They'll probably have an incapacitated power that really screws with his cards).
What cmschex said above holds a lot of truth to it. Apostate most of the time will be a fairly easy fight in my experience, and his Advanced Mode doesn't change him in any meaningful way really (relic spirits are easily ignored). But every once in a while you see exactly how swingy he can be. One really bad Profane Summons at the begining of the game will see you sing a far different tune.
LaCapitain is the same way at a lvl2 villain. Though she poses a more consistent threat than Apostate, Apostate at his worst is worse than Capitain at hers. Effigy + Orb is just about the last thing you wanna see.
I've had some horrible Apostate games where we seem to have no chance at all. He's definitely not easy all the time.
I still think his difficulty should be reduced, I mean, any villian has their really good games. Baron Blade getting devious disruptions at the right time can also be a very difficult or impossible threat, but that doesn't change the fact that he's usually quite manageable.
I hate to be all I've played more than you, but you might want to play a few more Apostate games before you make your final assessment. One easy game might be a fluke.
I lost hideously the first time I played Omnitron (actually the first couple of times), and while he can be difficult at times he mostly isn't that bad.
Similarly I won my first two Chairman games and no-one can say he's too easy.
I am still convinced that La Capitan should be a 3. I play her a LOT (as she is one of my favorite villains) and I rarely, if ever, have an easy game against her.
Fair Enough 
I always play her on advanced. She feels very much feels like a 3 there. But still no close to IL Matty or Pike. I think her normal mode being a 2 is very appropriate
I agree. We pull her out when we want a solid challenge. Never a 2 for us. She's about as bad as Dreamer in our experience.
I think hero count matters too, though - we play with three heroes (but two players) and Apostate has beaten us a few times (like, a couple, I think), but usually he's not too bad…sometimes he has a good run of cards but we can often managed to just about ang on and dig otrselves out from amid the pile of relics he's thrown out. We've never flipped him.
The Dreamer we don't tend to have a massive problem with - I think she beat us once or twice when multiple Dark Heroes were present but generally we do quite well against her.
On the other hand, La Capitan is one of those groan-worthy "oh no, not her" villains. We've beaten her a couple of times, I think, but mostly she kicks our arses.
And it's weird, but with both the Chairman and Baron Blade I can remember we used to beat them fairly often (Blade more so than the Chairman, of course), but these days we get overrun with Thugs and repeatedly nuked by Devious Disruptions and everything just goes to sh…you know, brown smelly stuff ;).