motherlove First, of all, the assumption the opponent controls what the Explosion user hits is flawed since, currently, there is no move in the game that forces a player to use Explosion when the opponent of such a move dictates. Well... except if you Taunt a 3-status + Explosion set, Torment a 1-move-only + Explosion set, Imprison all the moves except Explosion, or somehow Encore Explosion while keeping them trapped so they can't switch. The Explosion user can pick and choose when to explode, especially if the opponent doesn't know about the move. And can play around opponent switches just as the opponent can play around the Explosion user. "Oh, you're going to switch into my Refrigerate Explosion Kyu-B? It's now Baton Passing to Primal Groudon! Have fun!"
Also...
252+ Atk Refrigerate Kyurem-Black Explosion vs. 252 HP / 252+ Def Registeel: 177-209 (48.6 - 57.4%) -- 94.1% chance to 2HKO
I'm fairly sure Registeel doesn't run that EV spread since it gets murdered specially. Probably looks something more like...
252+ Atk Refrigerate Kyurem-Black Explosion vs. 252 HP / 128+ Def Registeel: 192-226 (52.7 - 62%) -- guaranteed 2HKO
Likely backed by... 252+ Atk Kyurem-Black Thousand Arrows vs. 252 HP / 128+ Def Registeel: 156-184 (42.8 - 50.5%) -- 2.3% chance to 2HKO
It doesn't really need to explode vs Registeel, especially if packing the right item. It can KO/force Registeel out with coverage and boom on your next Pokemon, getting effectively 2 for 1 with smart play.
Exceptions to this are non-Scrappy Normal Explosion into Ghost-types and Galvanize Explosion into Ground types or immune abilities.
You don't see Explosion much because it's the hardest 1 for 1 move to use. It requires smart play to get the most out of it, but with the right play, you can almost name your target on the opponent's team. Especially since they have to play super timid if they know about Explosion since very little in the tier can stomach the move. Meanwhile, for Tony, you can just go "lol go Chansey" and reset momentum, but you're only ever going to get 1 for 1.
As for your second point, a lot of it seems to assume the Tony player or D.Bond/Explosion opponent is smarter than the D.Bond/Explosion user. What's stopping the D.Bond/Explosion user from playing mind-games once the opponent knows the strategy with 50/50s of their own? Prankster D.Bond can easily pull crap like "priority Destiny Bond into super slow pivot", effectively stretching its presence out to two turns while getting a safe switch. Heck, they even have the advantage of being much more of a surprise. Tony, you can look at and go "Oh, there's Chansey and Zygarde, there's a good chance of Innards Out." and play accordingly. You can't go "Oh, there's Giratina, here comes Destiny Bond" or "There's Diancie, here comes Explosion." Additionally, the team can switch in if they're built correctly. SpecsRay has been nerfed this generation and we didn't need Tony to deal with it before, so why would the D.Bond/Explosion user be suddenly helpless against it this generation? There are plenty of defensive Pokemon who can switch in on SpecRay. And if the team loses because SpecsRay + Tony, I'd blame them not being properly prepared for Ray or for playing poorly. And, if all else fails and someone really, really wants to D.Bond or Boom, Focus Sash. I lost count of the number of times I wrecked an opponent with Focus Sash Prankster D.Bond Deo-A in the suspect by getting a 2 for 1. Harder now since we don't have CFZs to spam, but you can use stuff like Shedinja's offensive Innards Out sets to easily pull surprise D.Bonds on revenge KOers by tweaking them a little.
...also, the Destiny Bond nerf doesn't really impact much. If you're in a situation where you're having to spam it, you've gotten in a bad situation to begin with and the opponent wasn't going to attack you anyway.
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Towards more in general, here's why I feel Innards Out isn't a big deal and why I mentioned the other flavor of the month sets in previous posts: Innards Out is abusing the current meta teams, plain and simple. I mean, think about it: we're in an offensive meta just coming down from CFZs, which made things offensive as hell, and still have Comphaze for a little longer (which is most reliably answered by punching it in the face before it gets going) and also have Water Bubble as the next suspect, which is a super offensive ability that is nullifying things that should check it. Additionally, most players are accustomed to pivoting like crazy with U-Turn since it used to have no major drawbacks. Even most "stall" teams are basically just a bunch of pivot machines U-Turning over and over and over and over until they finally get an offensive Pokemon in a good position to attack once or twice, before going back to more U-Turn spam. So, is it any surprise that, when the tools came out to do so, someone found a way to seriously punish the meta for spamming the hell out of offense and U-Turn?
A number of us wailed loudly for bans and suspects on stuff like early X/Y Kyu-B and Protean Sash Deo-A since they punished the meta trends of the time dearly. But the suspects never happened and things went away on their own. The meta adapted in a healthy manner by finding a number of reliable checks and counters. And I feel the same will happen with Innards Out. This isn't like CFZ-spam, which utterly overwhelms teams that are not excessively prepared for it and can trivially bypass its counters. This isn't like Water Bubble, where you pretty much need to run Water Absorb to stand a chance at walling it. This isn't like Comaphaze, where if you don't counter it, one misplay means you'll be spending 32 turns doing nothing.
Guys, I'm asking you to listen to Flint about not worrying about Innards Out right now. Let the meta-stabilize after CFZs and, if banned, after Comaphaze and Water Bubble are gone too. Adapt. Is Chansey KOing you because you used U-Turn? Then stop U-Turning, you have Volt Switch, Parting Shot, and Baton Pass as options too. Sure, they're not perfect, but U-Turn clearly isn't anymore either. Are Innards Out sweepers knocking being too threatening? Get some good walls and lay down some residual damage instead of just spamming Shell Smash Power Trip. Are your sweepers getting KOed with random Innards Out? Then stop spamming them without proper scouting. You don't throw your boosted sweepers out willy-nilly when an Imposter or Shedinja is around if they don't counter them, so why would you do the same when you think Innards Out is on the prowl?
Also... it's worth noting, Innards Out isn't super super horrible. It gets one KO and resets momentum. 1 for 1 trades are not ideal situations, they're last minute "oh crap!" answers to stuff. You don't explode your Explosion user the first chance you get, you wait until it matters. If you're using Destiny Bond, you ideally want to go through the whole match never having to use it. If people are just throwing their Innards Out Chanseys at whatever is in their face, find ways to punish that careless behavior.
I dunno though, maybe I'm a bit biased since I play a variety of play styles rather than just hinging onto a couple of strategies in a certain spectrum, nor do I tend to try to mimic meta-trends. (No offense to you guys who do since a number of you are really damn good players regardless of how broad or narrow your strategies are.) So, it might be easier for me to adapt to threats than some others. I dunno, could be wrong, I never claimed to be right in every regard.
As for my stall vs Innards Out comments, when I mention stall, I mean full stall. Stuff like Adrian's Paranoid Stall levels of stall, which
might have a sweeper. These teams are Baton Passing and Parting Shotting everywhere, not U-Turning into things blindly because of stuff like Baleful Bunker can punish them too much. They do mostly passive damage, so Innards Out isn't doing anything to them and is basically being a dead slot if the stall player is smart. As for semi-stall, a smart Innards Out player would want to save it for their one or two sweepers/attackers since many of these teams rely on them to close the game and really struggle to do so once they're gone. Exceptions are those who are stopped by one one of the walls and they want to eliminate it. In which case, its the fault of the semi-stall player for bringing a move that can be punished that hard rather than Innards Out, IMO.