It's okay if I jump in at this point, right? Since the numbers on the poll show that the people following this thread aren't the same number posting.
Isn't the choice obvious in regards to the last move for the specially defensive set? While Thunder Wave will cripple Kyogre, the main issue is the fact that we still can't reliably kill it. If I'm reading the posts correctly, we aren't worried about its revenge killing cababilities. We're worried about 2 things; the rain it brings, and the raw power it can unleash on this team. Paralysis doesn't help at all with the first, while the second is only helped with a shaky chance of parahax.
Grass Knot, in my opinion, is the superior choice. Kyogre doesn't have access to reliable healing, so that damage is their to stay. An un-invested Grass Knot (it was a pain to calculate, given that the weight mechanic isn't included on the one I use) will do between 44-52% on a Kyogre with 4 HP. Even if the Kyogre has 252 HP, we're still doing 37-44%. Wear it down a little with attacks when it switches in, strike back when the iron is hot. I.E. When it's in KO range. This, in my opinion, would be a good solution to the Kyogre problem.