What the problem is, short of banning the weather abusing powers period to allow permanent weather (Sand Throw, Swift Swim, Chlorophyll), banning individuals really does nothing to rain short of banning them all. Kingdra has always been strong, it's 95 base stats in attack and defense across the board is misleading. It could always viably run Dragon Dance (which was in itself, hard to stop previously) in that it now gets a check in Nattorei (except Sleep Talk). But it isn't really uber without rain (hence why it's used there with Palkia as Palkia doesn't get Swift Swim).
And rain has so many abusers (Kingdra, Floatzel, Kabutops, Omastar, Qwilfish, Manaphy, Lapras, Gorebyss, Huntail, Ludicolo, Parasect, Toxicroak....). Banning Kingdra and Manaphy wouldn't be the end of the world for it. While it would lose two very helpful pokes that are good with and without rain (but phenomenal with), as long as perma rain is up, they still have insane speed and could fill in the gaps. Kingdra isn't the only poke that could abuse specs Hydro Pump (number 1 move of Rain Specs Kingdra without the -2 of Draco Meteor although none of the other waters get the Meteor as well). Lapras could do a Rest set efficiently (although Mach Punches aren't going to be fun unless it's Dragon Dance/Ice Shard against Bree), it just had been outclassed before. Qwilfish could join the ranks as the fastest Destiny Bonder and Poison Jabber of doom (it is amazing that Qwilfish isn't even mentioned by people, it pretty much laughs at every priority type, has the same speed stat as Kingdra, the fastest Destiny Bond in rain short of that Custap Berry Wobbuffet, Poison Jab is death to grassers, clears up Toxic Spikes as well as Toxicroak...), Poliwrath can still Swift Swim Belly Drum (lol, I didn't even know it could do that until recently) and on and on and on....
So Rain is barely neutered really by only removing Manaphy and Kingdra. While it does lose some of it's most powerful sweepers, it still has plenty of them. And it doesn't reduce it's brokenness at all, just changes it's method.
Fire would get more neutered with the removal of Venasaur and for not having nearly as many good abusers of rain (or inducer for that matter) but it still has Mebjuka, Tangrowth (essentially slower and less special defensive but much more physically bulky Venasaur), Hidiharuma, Charizard, Heatran, Moltres, Exeggutor, Shiftry, etc. But it could still viably work.
Sand is still broken. Two abusers (that are actually good and can fit on any team for the most part except another weather themed one), Sandthrowers like Sandslash and Doryuzu who break the speed barrier, Landlos has Sand Power, Swords Dance, Bulk Up and is bulky and does heck with stab Earthquake and Stone Edge for coverage; Garchomp is just an awesome pokemon (whose most common set now apparently is Swords Dance) who can Swords Dance, Revenge Kill, and is just irritating to hit in sand and has caused losses because of that, Gliscor takes Breloom and can Swords Dance and beat you with stab Earthquake (and has Sand Veil for Sand and Roost or Poison Heal for outside or inside sand). It gives a rock special defensive boost (which really only honestly helps two Pokemon, Tyranitar and Terakion. Nearly everything else doesn't usually help) while Hail gets nothing. However, unlike many other weather pokes, they aren't near useless without sand unlike many Swift Swimmers, their weather is the easiest to set up (except against Rain which it will be hard to switch in, especially if they actually have the move Rain Dance which all weather teams should have their respective weather moves just in case their inducer dies or you can't risk a switch in. But they'll never see it coming and just when they thought they had hope of winning after managing to kill your auto, you pull that baby out and watch their joy die since by that time, you probably could finish them off.), etc.
I thought of only Hail for a second, but even Hail would be dominating as the only weather. A well built Hail Stall will tear people apart since it wouldn't have Sand or other weathers to ruin it, has Kyurem to 1-2 hit ko everything with Choice Specs 100% accurate Blizzards, will stall you to death with things like Walrein, Toxic Spikes, other hazards, etc. Abomasnow is a pretty decent pokemon and can throw Blizzards and Subseed or be Swords Dance or Scarf. (Swords Dance Jolly can beat Adamant Breloom with Ice Shard for the lols and giggles.) Ice has some good users Mamoswine, Walrein, Kyurem, Regice, and a good Hail Team isn't all Ice cause it will have things like Tentacruel, Gliscor, Breloom (Poison Heals), etc to take the Fighting moves that are the bane of Ice types.
And if you remove Rain, Sand will be dominant. If you remove Sand, Rain assuredly will. If you remove Rain and Sand, Sun can rule the coop easy. If you remove Sun, Hail will be overpowerful (the only thing that kept Hail from ruling was auto Sand before and if you remove auto Sun and Rain as well, Hail would be ridiculous).
The only thing to do then is ban all the AUTO-WEATHER abilities. Rain and Sun are still useable with the traditional Sunny Day and Rain Dance. If you want Sand, you should run Sandstorm and Hippowdon and Tyranitar are hardly ruined as good pokes at all for not having Sand (and in fact could then be used on weather abusing teams). It makes Doryuzu much much much much less broken, Garchomp/Landlos/Gliscor don't need sand although don't mind taking advantage of it and Garchomp wouldn't be a luck hax risk of missing and then being swept by it. It never really helped most rocks except Tyranitar or Terakion because many still had too weak special defenses without a ridiculous usage of SDef evs. Hail is weak without Snowstorm but it isn't like anyone was really using Hail (because of Sand/Rain and now Sun) to begin with. It just had to be ban all auto-weathers or none. OU is beginning to look a lot like Ubers (with their Weather and disregard of weather metagame) except minier and weaker sun/water inducers and more sand/rain oriented than rain/sun oriented.
Except that in OU it is much harder to change the weather than there and so there is that problem.
Neutering the auto-weather weather may cause some strategies to disappear (who cares about Parasect, Toxicroak, and Subseed Ludicolo usage in comparison to nightmare infinite weather Chlorophyll/Swift Swim abuse? And it's not like strategies like auto-Hail were being implemented due to the annoyance of other weather so completely killing it makes no discernible difference to the overall game). But it is worth killing a few to stop the overall infinite weather nightmare (and they weren't good in comparison anyways to the attacking prowess terror anyways). And actually it would allow traditional and newer usages of the move Sunny Day, Rain Dance and set up strategies. Sunny Day would be worth finding a way to set up for 8 turns unlike previously as it has better abusers in Hidiharuma, Venasaur, and special attack boosted Charizard. There probably is a reason why they stuck drought on Ninetails instead of something actually useful. Rain Dance had always been used on things like Electrode, Kingdra, Ludicolo, Brongzong, etc. It now has Mischievious Heart users to set it up as well with priority and so does Sunny Day (although lesser spread but Sableye and Erufuun do have it).
So weather being ruined by losing their auto-ability inducer (with the exception of Hail because that is even more of a useless move than Sandstorm which at least some things might want to attempt except on Kyurem which could attempt to use it for 100% Blizzard) is NOT TRUE. It is easier to find things to attempt to set it up than it is trying to play against a permanent weather format when unless you use the same weather team, leaves you at a disadvantage, facing much faster things which also get a power boost as well.
Unless one wants to ban Swift Swim/Chlorophyll which really would neuter them and make weather much easier. But one shouldn't kill Swift Swim/Chlorophyll when it is easier (and more fun as a strategy to play/fight) to set up 5-8 turn weather and use a move to do so instead of having weather on turn 1 without doing anything and already primed for a sweep. It would create more ways to set up weather which are pointless in the face of auto permanent weather and any good weather team should carry multiple users just in case (even permanent to watch the opponent cry if they manage to switch it, only to turn it back).
The fact is that weather FORCES a weather game and anti-weather and restricts anything else to the neither regions with the exception of kinky things like Trick Room (which is lesser used anyways although it is fun). That is what you call overcentralizing. In ubers, they have things to kill weather pokes and things to double abuse both sides and work in all, and an actual good Cloudy Skies. (Zekrom, Palkia, Rayquaza). It also is torn pretty equally between the weathers now (prior it was definitely rain oriented) with support like Ho-Oh, Reshiram, and Zekrom for the sunny side as well as an actual good Drought (Groudon). Both weathers (and anti-weather) can actually stand a chance against one another unlike the definite Sand/Rain (or Rain/Sand) slant of OU which definitely overpower.
Non-Uber Cloudy Sky users are pathetic for the most part except maby Lickilicky. I guess Golduck and Altaria are okay...but in OU? Um...never play Altaria against a Sand/Rain/Hail team or certain Sun abusers. Which makes Altaria...well bad. Golduck could work against certain Sand pokes but Doryuzu still outspeeds and could kill you (Jolly Life Orb), Garchomp still outspeeds and could carry Yache (or be boosted), Landlos still outspeeds, and if any of those had a Swords Dance, they definitely kill Golduck. Golduck certainly isn't switching in against things like Venasaur or Mebjuka, or even Choice Band Hidiharuma Flare Blitz which can still potentially ohko even without Sun and being resisted. Golduck would not like Kyurem, potential Abomasnow Wood Hammers, Tentacruel, Breloom, etc.
The only potentially good Cloudy Skies is Lickilicky who still must fear boosted moves and would need to carry a ton of special defense to handle special which leaves it more open to the strong physical things like Breloom, Hidiharuma, anything with Swords Dance on Sand (although they'll need Life Orb to guarantee without Sand or carry something against potential Icebeams unless it's Terakion who would massacre it with or without boost unless it is carrying max hp/def but with Life Orb would still potentially ohko even that without Swords Dance), etc.
Trick Room might potentially be good, since for 4 turns (counting the turn of Trick Room), it would be going first and many weather teams have defensively weaker Pokemon. However, you'll have to survive an attack to use it since you're going last and taking sun/rain boosted stabbed attacks are tough, even with defenses like Porygon2 (Choice Band Hidiharuma can ohko it with Sun Encourage Flare Blitz, even with Max hp/Def and Evo stone and no Porygon runs a spread like that). Then you'll have to finish them off in 4 turns, while still fending off boosted attacks if you don't ohko every round, and then have to somehow manage to reset it without dying once it returns to normal. That...is the difficult part. Trick Room or Cloudy Skies is in no way a surefire counter (but Trick Room is probably somewhat more effective than Cloudy Skies). It won't kill a weather dominated game.
Oh god, I just wrote an essay on why auto-weather is broken.
Ps. Nattorei is a horrible, horrible, horrible defense against a Sun team, lol. And relying solely on Nattorei to block all water and attempting to kill Politoad and then manage to change weather is bad and horribly overpressurizing since if Nattorei goes bye bye, you'll likely die. And switching in Nattorei against a physical Swift Swimmer will NOT work since boosted, they will kill you. Have fun facing Belly Drum Poliwrath, Swords Dance Low Kick Kabutops (who will die if it attempts to switch in on Natt but Natt can't switch in on it), etc. Heck, if they have Cloyster, they can turn your Nattorei useless although Cloyster itself isn't a Swift Swimmer.
