So personal thoughts after a couple days of playing (not that much - I've been watching a fair bit but I haven't had a chance to play bc of a billion other responsibilities D:) - I originally didn't think Manaphy was an issue, and I still don't, but I do think rain is a massive problem and would like to push for a ban on Drizzle. Here are the two obvious big ones:

Manaphy is the destroyer of fat teams everywhere, much like it has always been. Defensive counterplay is limited to Mantine, Unaware Clefable, and Shedinja... and Clefable is cheesed by Skill Swap anyway so lol (edit: i thought shedinja was too but i GUESS NOT). It trucks balance with ease, though stall doesn't actually have a huge issue with it because of the former two Pokemon being pretty much staples. Kingdra shits on any and all offense, particularly those that have the nerve to drop the one offensive Pokemon capable of soft checking it in Azumarill. Together they are the cream of the crop and what makes rain broken, but I'd like to present a few reasons why I don't think we should ban them.

These two Pokemon are obviously not as bulky as Manaphy, Crawdaunt in particular is very frail and Gatr is fat but can't compete with 100/100. They make up for it, though, in their ability to muscle through -every Pokemon in the game- without fail. Here are a few Pokemon that could theoretically fit on fat teams that get absolutely mauled despite seeming like they may be checks. Some calcs require an SD boost which you conveniently can freely get on Pokemon like Blissey and Slowbro/king.
252+ Atk Life Orb Adaptability Crawdaunt Crabhammer vs. 252 HP / 252+ Def Clefable in Rain: 390-460 (98.9 - 116.7%) -- 93.8% chance to OHKO
252+ Atk Life Orb Adaptability Crawdaunt Knock Off (97.5 BP) vs. 248 HP / 252+ Def Mantine: 257-304 (68.9 - 81.5%) -- 50% chance to OHKO after Stealth Rock
252+ Atk Life Orb Adaptability Crawdaunt Crabhammer vs. 252 HP / 252+ Def Skarmory in Rain: 252-299 (75.4 - 89.5%) -- 12.5% chance to OHKO after Stealth Rock
+2 252+ Atk Life Orb Adaptability Crawdaunt Knock Off (97.5 BP) vs. 252 HP / 252+ Def Tangrowth: 354-416 (87.6 - 102.9%) -- guaranteed OHKO after Stealth Rock
+1 252+ Atk Life Orb Adaptability Crawdaunt Knock Off (97.5 BP) vs. 252 HP / 252+ Def Salamence: 356-421 (90.3 - 106.8%) -- guaranteed OHKO after Stealth Rock
+2 252+ Atk Life Orb Adaptability Crawdaunt Crabhammer vs. 252 HP / 252+ Def Azumarill in Rain: 368-433 (91 - 107.1%) -- guaranteed OHKO after Stealth Rock (if you wanted to run this for some reason??)
This doesn't even begin to cover the fact that Jet gives you a great offense MU, nuking Blaziken, Weavile, Infernape, Nidoking and even dropping Garchomp in a single hit at +2. It also comes very close to dropping
Latios, 1 SR hit + 1 Life Orb hit or 2 SR hits makes it a reasonable or even favourable roll.
Feraligatr does much of the same thing but doesn't even need to take Life Orb recoil, making full use of its good natural bulk. It does just barely miss out on most OHKOs but it can tank hits from the Pokemon it's hitting easily (for example, Clefable's Moonblast doesn't even 2HKO it after Stealth Rock ever):
252+ Atk Life Orb Sheer Force Feraligatr Liquidation vs. 252 HP / 252+ Def Clefable: 196-231 (49.7 - 58.6%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery
+2 252+ Atk Life Orb Sheer Force Feraligatr Ice Punch vs. 248 HP / 252+ Def Mantine: 237-279 (63.5 - 74.7%) -- guaranteed 2HKO
+2 252+ Atk Life Orb Sheer Force Feraligatr Liquidation vs. 252 HP / 252+ Def Skarmory in Rain: 378-446 (113.1 - 133.5%) -- guaranteed OHKO
+1 252+ Atk Life Orb Sheer Force Feraligatr Ice Punch vs. 252 HP / 252+ Def Salamence: 655-775 (166.2 - 196.7%) -- guaranteed OHKO
+2 252+ Atk Life Orb Sheer Force Feraligatr Ice Punch vs. 252 HP / 252+ Def Tangrowth: 322-382 (79.7 - 94.5%) -- 50% chance to OHKO after Stealth Rock
+2 252+ Atk Life Orb Sheer Force Feraligatr Liquidation vs. 252 HP / 252+ Def Azumarill in Rain: 277-328 (68.5 - 81.1%) -- guaranteed 2HKO after Stealth Rock
Much like Crawdaunt, Feraligatr also has an Aqua Jet that sends anything weak to it (and most things neutral) to the shadow realm whenever the rain is up.
Basically I don't think Manaphy is the problem behind Rain's incredible fat MU but rather just the tier's kinda middling water resists (and by this I mean we don't have Toxapex...), anything with fatbusting capabilities will just go bananas. Manaphy has the longevity advantage over these two for sure but unlike Manaphy they just... break the entire tier on the spot.

There are a lot of Kingdra alternatives - Golduck is the one I'm talking about here because it's the most directly comparable, but there is Ludicolo, Kabutops, Mantine, Omastar, Floatzel, Qwilfish... you get it.
Golduck shares Kingdra's statline as far as the most important ones go: a solid 85 Speed tier, and a very workable 95 SpA. This makes its Surfs/Hydro Pumps just as capable of cleaning up offense as Kingdra's, with its main shortcomings being two things:
a) it's less bulky
b) it's not able to OHKO the Lati twins
It makes up for this in some ways, mostly an Ice Shard resistance instead of a neutrality and the ability to switch up its game with Calm Mind if it wants. It pretty much performs the exact same role in my testing and as such I don't think banning Kingdra will really help that much. Doesn't even begin to mention the others I listed above... Kingdra is not the broken element but rather the best of the broken elements, if that makes sense.
Basically I think we really just should get rid of Drizzle and leave it at that, nothing else in the meta feels really broken to me except maybe Latios (which is also powered up significantly by Rain anyway) and I'd rather let it settle beyond that. I'll be keeping an eye on it during the Charity Bowl for sure. I'm glad people are enjoying this meta so much, it's been a blast to play for me!!