NP without the third coverage move is terrible for the reasons I just discussed. And Thunder is bad, Tbolt is better when weather is changed. You can't really expect to go out there and hit anything with Thunder and HP Ice, can you?
If you NP on the switch and the opponent chooses to switch into comething faster, you're screwed.
If they switch into a wall, you're free from status for a turn.
With something like NP Thundurus, you want to be able to get a hit off before something comes in to revenge you (and it is easily picked off due to its frailty). Thunder, as has been pointed out countless times in this thread, doesn't make a difference against Blissey/Chansey as you need Focus Blast for them anyway. And if you think Thunder lets you get past Ferro, you're dreaming; Gyro Ball 3HKOs, you need some extreme parahax to kill it.
Hp ice does nothing to Ferrothorn, Quagsire and Gastrodon. Thunder isn't reliable against TTar (actually it isn't reliable at all unless you can keep rain up 100% of the time). Thundurus needs a 3rd attacking move and even then you always have trobules choosing between focus blast and grass knot. Focus blast gives better coverage obviously but it's accuracy is really a tragedy sometimes.
If we're talking how Rain is always going to be around, you need to adjust your calcs for Chansey.
Let's turn around and talk about how well Thundurus is going to keep full health during the match, then; if we're talking two layers wearing down Ferrothorn here, in addition to needing 3 turns of setup + attacking just to knock it out, then it shouldn't be unreasonable to assume that Thundurus is going to be taking SR damage and then put into 2HKO range by Gyro Ball. I don't see how that's any less likely than the scenario you've pointed out. The idea is to be able to set up on Ferrothorn, a poke which according to your typing and resistances should theoretically be easy set up bait, and should be in abundance according to your theory that rain is everywhere.
And to expect that rain is going to be everywhere is far too arrogant a position. We haven't even considered Hail here, which, unsurprisingly really screws up Thundurus. It's interesting to note that +2 LO Thunder OHKO's Ttar, while having the same accuracy as Focus Blast, but you really need that coverage (hitting Abomasnow is a godsend). Since you seem to assume that Thundurus is always going to be around at 100% health, then you can survive Aboma's Ice Shard and then Focus Blast it.
EDIT: Alright, so according to calcs it seems as if Chansey needs to run a bulkier spread than 252/0+. The fact hasn't changed though that Sub doesn't help the NP set when 'smashing' Chanseys.
About substitute, it is generally a good idea for NP+Sub, but not as solid with agility. The point of substitute is so that you can gain more than one boost. Quite a lot of walls carry sets that don't even have attacking moves- Blissey, Chansey, etc. Of course you're not doing much at +2, but while you're getting there, neither are they. However, assuming that your wall doesn't have attacking moves is not very smart, especially for the frail T-T. What else does substitute allow you to bypass?
-Trick
-Status
-Weak moves
While NP doesn't give T-T a boost in any of it's defensive stats, should it just have two turns to set up then you're virtually unstoppable.
Back to the 'blissey/chansey with no attacking moves' example, let's say they DO have an attacking move- seismic toss. Of course that can break one of your subs and WILL break one of your subs as you set up- but tehn leaves the opponent in a mindgame. Should they ST again to break another incoming sub, or should they status you, hoping to catch you while you try to set up one more time?
The obvious answer would be to attck, because even if T-T doesn't sub you can still cleave off a nice chunk of health before your Blissey goes down. Now, as the player with T-T you could predict that and go for another NP. What I'm trying to say here is, because of T-T's tremendous amount of power after just two boosts, it can decimate most of it's walls. That's why substitute is important- it helps you get those two boosts.
Unless you're running into teams with two or more of Magnezone/Rotom-F/Rotom-H/Lanturn/Shedinja, BoltBeam doesn't suck. Thundy's only coverage issue is whether to run Focus Blast or Grass Knot, in which case Focus Blast is almost always superior. I guess one could make a case for TBolt / Focus Blast / Dark Pulse, but being able to whack the Pokemon that resist Thunderbolt with HP Ice is too good. It also gets Sludge Bomb/Wave, which really don't offer much, and Incinerate which is just pathetic.If anything, I'd rather take that opportunity to Agility, and after trying out that set, I realized that the lack of coverage plainly sucked.
Unless you're running into teams with two or more of Magnezone/Rotom-F/Rotom-H/Lanturn/Shedinja, BoltBeam doesn't suck. Thundy's only coverage issue is whether to run Focus Blast or Grass Knot, in which case Focus Blast is almost always superior. I guess one could make a case for TBolt / Focus Blast / Dark Pulse, but being able to whack the Pokemon that resist Thunderbolt with HP Ice is too good. It also gets Sludge Bomb/Wave, which really don't offer much, and Incinerate which is just pathetic.
EDIT: I've been using a mixed Agility Thundurus-T with Superpower recently, but found that Focus Blast outdamages it against most things even in Sand. The only ones that aren't hit harder by Focus Blast are either hit even harder by Thunderbolt or HP Ice, are Normal-type fatasses who still take decent damage from Focus Blast (and should be removed anyway) or are rarely seen in OU (Gallade, basically). Superpower's only benefit lies in a bit of a surprise factor and accuracy. tl;dr don't go mixed when using Agility.
You don't bring Thundy-T in early game, boost up, and try to take down your counters from 100%. Like every other sweeper, you weaken the counters with hazards or Pokemon that hit the same target to overload them. On offensive rain teams that is really easy to do with Starmie and Tornadus-T because teams usually rely on Ferrothorn (not really Tornadus)/Blissey/Chansey to take them on. The 2HKO's with Thunder aren't to show that Thundy-T can beat them in a 1 vs 1 situation from turn 1, but at a point where they are weakened.
Expert Belt sounds like a great idea, as whenever i see a Thundurus-T using Volt Switch without taking LO damage i assume it is choiced.Okay so I tried SubPlot Thundurus and I find it underwhelming. IMO LO/Expert belt is the best. I'm actually using E belt right now and it kicks ass. Each time this guy comes in I know I'm going to dent or kill something which puts a lot of pressure on my opponent. It's also really good at faking choice. I don't know how many times my opponent has tried some ground type into what he thought was a choice locked Volt switch, just to get OHKO'd by a HP Ice or Grass Knot. I went ahead and did a test alt just to see how well this set does and, over the course of 12 battles, he has gotten it to rank 16. So my summary would be this: NP variants are best for beating down Stall, Agility is for cleaning HO, Choice/LO/Ebelt are the best sets for general purposes. In any case, preparing for this guy is a headache when team building and a very risky game of prediction when battling.