Swift Swim+Drizzle made entire teams broken; Manaphy+Drizzle only makes Manaphy broken.
No, it didn't. Under Swift Swim, Kingdra was broken, and possibly Ludicolo and Kabutops as well. It's as much a matter of individual Pokemon as any other ban. Back in Round 1, if you were to build your team around a Deoxys-N sweep, it wouldn't be your team that was broken, it would still be Deoxys-N.
All bans are arbitrary to some extent, but trying and pick out the individual Pokemon that "break" weather would just be too much. How do we know Kabutops would be broken without Kingdra and Ludicolo to back it up? Outside of doing numerous rounds of testing, we can't possibly know. And once we sort those three out, what if SD Qwilfish is too much to handle as well?
Sure SwSw Luvdisc isn't broken, but do we really have to spend 3 or more rounds of testing just to draw the (extremely arbitrary) line between the "broken" Swift Swimmers and the balanced ones? Given the fact that we already have a system in place that works incredibly well, I would say no. Pretty much every ban we have in place could be mediated with the outcome being a metagame that is arguably "better," but seeing as the bans that are in place already work it's not worth the effort.
No different from any other bans. And given that this generation has reached a point of clear stability so quickly, I think there's a very high chance that most of those Pokemon will not be an issue. It could take three rounds of testing, or it could just take a single round where we ban Kingdra, either in combination with Drizzle or entirely, and find ourselves with a completely stable metagame without any more bans, where Ludicolo, Kabutops, and Quilfish are top OU threats but very much reasonable for teams to deal with, and where others such as Omastar and Floatzel are also OU-viable, being permitted due to their not being broken, and being viable due to not being overshadowed by Kingdra.
What cannot be ignored is that Swift Swim users are not equal, and they cannot be treated as such. Kingdra has the best offensive typing in the game, and defensive typing resulting in only the one weakness that matters to it least. It has the highest BST of all Swift Swim users by 41 points, and those stats are distributed extremely well, resulting in no weaknesses whatsoever stat-wise and enough offensive versatility to do hack through just about anything. It is by far the most dangerous Swift Swim user, and its sheer power and even the threat from its presence makes anything on a team with it a drastically bigger threat. The problem is not Swift Swim, it's not Drizzle, and it isn't th combination of Swift Swim + Drizzle. It's Kingdra. Whether that problem is Kingdra itself or Kingdra + Drizzle is for PR to decide, but Kingdra needs to be addressed directly.
Ludicolo and Kabutops should be set up as Suspects - either entirely or only in Drizzle, whichever PR decides. That way, whether they turn out to be broken without Kingdra or not, we can find out our answer in a single round. We shouldn't expect anything else to be a concern. We've seen no evidence for any Swift Swim user other than those three being a Suspect in the slightest, so we shouldn't proceed with the assumption that they will be.
And no, the current system does not work. We are restricting the usage of Pokemon when we have no evidence to support them being broken. For some of those Pokemon, we are quite confident that they are indeed not broken. For others, we are aware that they are OU-viable. This has never happened before. The reason it happened is a good one - to test whether or not Drizzle would be broken without its top Swift Swim sweepers, and we have found that it is not. However, to continue with this as a permanent solution would be an unacceptable violation of Smogon's philosophy to avoid bans as much as possible and to only apply them to Pokemon for which a ban is necessary.
There are solutions to this problem, and they are not ones that are unreasonable to implement. There is no reason for Smogon not to change its focus with the bans from the decidedly not broken combination to individual Pokemon.
The point was that Swift Swim + Drizzle when played competitively (a fair assumption to make unless you want to criticise tiering) was making the team as a whole broken. Would you argue that Politoed alone was broken? How about Kingdra or Kabutops or Ludicolo? The issue here is that individually these Pokemon aren't broken, but when you have that combination of Drizzle and a multitude of Swift Swimmers you have a team that is broken.
Individually, Kingdra in Drizzle is absolutely broken as a sweeper. If Ludicolo and Kabutops can lead to a broken team, it is because they too are individually either broken as sweepers or as offensive support for other sweepers, but that remains to be determined.