Umm... manaphy is also devastating with calm mind to add to its bulk, not only used as a sweeper. It does have acid armor if you prefer
Manaphy can also use energy ball, taking away from your idea of using bulky waters to counter
skymin is banned in OU and shaymin doesn't have any boosters + its typing to make it as viable
Same with victini, v-create lowers its defenses and speed so you aren't likely to get hit twice. SR and the fact that most of the metagame's typing works against it keep it from rising.
Also, I am sorry but you are very mistaken on your claim about weather. And using the "top 10 on the ladder" as your evidence for that is very misleading and quite frankly not a good estimator.
I do appreciate you laying out a well-formed argument like that so I will take the time to address all of the other things you pointed out
Natural cure isn't that amazing, shaymin isn't physical so burn doesn't do too much damage, toxic is well, toxic and would be "reset" upon switching back in and paralyze isn't as useful on a not as fast pokemon. Sleep is sleep Iguess... fine, one status. Hydration is much better as it does not require the turn to move out and the turn to switch back in, rest is an auto full restore which is insanely useful as you need to have a guarenteed 1 or 2 KO in order to beat it.
On that note, it makes scald even more useful as it burns the opponent and thus requiring an even stronger pokemon to beat it. If the calm mind set is used, good luck finding a physical attacker that can beat it.
And again, lol at thinking that rain needs something like manaphy to balance itself. Whilst I do not think weather is OP, I know that there are many who do. Considering that not everyone, certainly not all of the good battlers, ladder, it isn't a good indicator.