For those with Honchkrow problems, I suggest using a WoW/Reflect Rotom. Since most Honchkrow aren't using Night Slash anymore, it's pretty much free to switch in at any time and set up a wall or spread status. I've been using a Dual Screen/WoW/TBolt Rotom on my current team and it's been amazing.
Rotom isn't that great a counter really, especially without any recovery. Any version that can outspeed is taking just under 50% minimum from Brave Bird, and therefore can only switch in once reliably. God help you if they happen to be carrying a MixDoom on the same team.
Anyway, I'm glad I'm not the only one who sees how overpowering Honchkrow is now. Brave Bird has had more of an effect than even I anticipated, and will surely be the next suspect. Only solace is that now Rhyperior might be coming down, so UU would now have a decent check that can stay offensively minded.
NP Missy can be good, but I agree that dropping Substitute invites way too many risks in the current UU metagame. It has got better though no doubt, as long as people realize that it still has the CM option and Nasty Plot serves to make it less predictable as an offensive threat.
Really not impressed about Aggron so far though. A worrying percentage of the metagame outruns and carries Water / Ground / Fighting moves, not to mention all the bulky Ground and Fighting Pokemon. I actually think that Relicanth is still a better fit to the metagame despite being weaker. Ambipom's Low Kick is a measly 60 BP, Honchkrow's Superpower doesn't OHKO, and STAB Aqua Tail provides better secondary coverage than Aggron could ever hope for, among other advantages.