He went to Groudon as I Sub'ed, I used Hone Claws as he broke the Sub and then Outrage next. That turn he went for SR, so Groudon was 2HKOed.
Thunder only kills Lugia if it's raining, and Lugia can be faster and so Roost on it. Problem is the full paralysis. And Lugia can Whirlwind / Dragon Tail, so it doesn't lose most of the time.
Guess what Darkrai's OHKO move is? :)
Manaphy has three things over Kyogre: Tail Glow's +3 SpA, Hydration + Rest and base 100 speed. It's not the same as preparing for Kyogre. Simple example would be a slower Pokemon using Thunder on Manaphy. It can CM, and then Rest, and then CM, and then Rest, and you can't hope for the paralysis. Scarf Thunder doesn't OHKO Manaphy usually, so it can Rest to scout, see it is slower and deduce it's Scarfed, and then go to Electric resist. Grass Knot doesn't hurt Manaphy at all while ravishing Kyogre, Wacan + Tail Glow defends against Thunder (most common anti-Manaphy move), etc.
Does SkarmBliss work in Ubers? I've not tried it, but at the moment Skarmory looks rather under-utilized, and the best partners to Skarmory look like the pink blobs (can also scout Dialga sets without instantly dying).