I don't see what the true issue with Manaphy is, when we have Pokemon without a large number of counters dominating the game as it stands.
Manaphy faces the prospect of carrying Rest+Tail Glow, but then only two attacks, making it walled by a lot more.. and not being able to support its own rain. If it tries to support its own rain, it has the same issues, and possibly the lack of Tail Glow. Thus you're using a bulky water, and Manaphy is great at it.. but it has counters in that case.
Then there's this..
If Manaphy runs its most dangerous set, Tail Glow+Grass Knot/Ice Beam/Surf(or insert random HP..), it has no recovery move, depends on others to setup Rain Dance, and is picked off by revenge killers.. just like say.. Garchomp; Which also has few counters, and possesses an absurd amount of power with Sword Dance? Garchomp of course does not as heavily
depend on weather support to totally break its walls.
Over-centralizing is a ludicrous argument, in my opinion. Every team will carry a counter, or revenge killer for a powerful (over-centralizing?) Pokemon. Over-centralizing is not the same as too powerful for OU. Not every team would have to carry a Manaphy to win, just as not every team carries a Tyranitar, Lucario, or even Blissey to secure victory either. Yet teams would carry counters for all those.
If Manaphy is tested and starts running through every team insight, send it back to ubers. I think it deserves a shot if only to diversify the game, not limit it.
Lapras seems viable as a counter, but that would be centralizing the game just to counter Manaphy. I do agree that Manaphy is not the most unstoppable force however.
Lapras can't counter any Manaphy that carries Grass Knot, as was just discussed on the last page. Lapras is 485 lbs. (220kg).