Firstly, I don't think you got my point. I'm not arguing whether or not those things are broken at all. What I'm arguing against is this:
And this:
I'm asking what is it that makes the banning of a move from many pokemon okay yet banning a move from a single pokemon "not simulat(ing) the game" when in fact both are the same thing--the mutual agreement not to do something in a match. I'm asking what exactly makes one a legitimate proposal and the other not, as simply saying that the former is legitimate and the other is not is not sufficient proof for that argument. (By the way I do think Evasion, Sleep, and OHKO clause are fine and that having Skymin be OU just without Seed Flare is stupid, in case you're wondering). If we are to make a distinction saying that we don't, say, "ban specific things so that a certain pokemon can be OU" but instead "ban specific things so OU doesn't become a total clusterfuck" that would be a much more compelling argument, which I think is pretty much what we do now.
Secondly, how is something that's broken not unhealthy for the metagame? Isn't that the whole reason we ban things to begin with?
The difference is, we have banned Evasion/OHKO from the game period across all tiers as they make the game uncompetitive in and of themselves. Seed Flare in and of itself is not uncompetitive, otherwise Shaymin-L would be facing Ho-Oh and Rayquaza rather than Heatran and Salamence at this point.
The point I'm trying to make is this. We are used to banning things if they are broken under a set of general "common battle conditions." There is a difference between Shaymin-S spamming LO Seed Flare followed by an Air Slash and sweeping, and using a Rapid Spinner, Pursuit user, and weather setter to allow, say, Manaphy to sweep.
This generation...what exactly
are common battle conditions? It definitely isn't Sand + SR like it was last gen. It could be Sand + Spikes. Rain + Spikes. Sun, period. Rain + Toxic Spikes. Weatherless + Spikes + Stealth Rock.
And then with the pool of pokemon having significantly increased, there are new checks to old threats and old checks to new threats alike.
In the majority of conditions, I do not believe Manaphy to be broken. The loss of Hydration is really big for it, since there are plenty of faster threats and if it wants to support itself, it loses a coverage option (which is a severe cost considering the threats running rampant nowadays). This situation is very similar to Kingdra and the Swift Swimmers. Kingdra is far from broken outside of Rain, no one will argue that. Only in one of several conditions does it become broken, so that particular scenario is prevented from happening in the first place.
Before people try to apply this to the Gen 4 metagame, think of this. Outrage is not broken in and off itself, so we could not ban that on Salamence to keep it OU; Mence had to go. Yache Berry is not broken in and of itself, so we cannot simply ban Yache + Garchomp; Chomp had to go.
The same would apply to the case of Manaphy. As far as Manaphy / Kingdra / etc taking advantage of opposing Rain, that is a risk that a Drizzle user takes when constructing his team and should prepare adequately. Furthermore, relying on opposing Drizzle would be a poor strategy and few would try it.
And I really don't see how adding a viable pokemon to OU (or in this case keeping it in OU as it originally was, if it doesn't prove broken) is unhealthy for the metagame.