I honestly think that Agility instead of Nasty Plot makes for a better Thundurus-T set.
When I look at the base speed after 252 invested, I'm not as worried about speed. There are revenge killers (i.e. Scizor) who can still be potent at 190 speed. While he is frail, he still garnishes the opportunity to boost in either speed or spatk when he inevitably causes a switch. It just takes really careful prediction, or you're right, he will get smashed fairly quick.
You're right on the Dark Pulse part, and I never really thought to run him on a Rain team, so Thunder absolutely makes more sense. If Dark Pulse does more damage than Thunderbolt, then why not leave it there, throw in Agility, and revenge kill?
Would a redistribution in stats make more sense for say, a bulky Thundrus? Minimal investment in SpAtk, but beef him up and work on his HP and defenses?
I caught the defense drop like, right after I posted this and went back to make modifications. He's Modest now. :)
Thanks for the tips!