Choice Specs Dialga and Palkia can both 2HKO with Thunder, while shrugging off Scald with ease. Barring a Scald burn, any really powerful Ubers physical attacker (examples including Rayquaza, Zekrom, and Groudon) can break through Kyogre with relative ease.
As for a damage calculator, use Honko's:
It's the best, in my opinion.
"May the odds be ever in your favor"
"WTF HAX NOOB"
The hills are alive with the sound of PS ladderers.
Come over and help out with the Ubers CCAT