I didn't read any discussion on this, but from personal experience, Rudra's was an all around subpar WS, whereas Mercy Stroke excelled inside and outside of Abyssea. I've seen higher Mercy Stroke numbers in both cases, both with and without SA/TA. Highest Mercy Stroke I saw on Colibris was 2.8k (without SA/TA), if you discount the 25% bonus, that's still over 2.2k WS. I could barely beat that on WAR with 2hr up (highest Penta Thrust I did was 2hr'd 3.6k, 2.6k without 2hr, and that's both including the 25% bonus). Note that this was all at 75.

Recently we did some sea NMs with a Rudra's THF with pretty good gear, he only recently got his Twashtar 90, so he was testing a few WS builds and playing around. The results were less than impressive, I have it in my logs, I'll go through the parse soon to compare. Mercy Stroke on the other hand was putting out rather high numbers (and pretty consistent too).

Again, this is not math based and I have neither WS so can't try stuff myself, just from my experience I found Rudra's Storm not the least bit impressive, whereas Mercy Stroke often outdamaged a fully buffed Evisceration inside Abyssea.