I must admit, I have only battled one Manaphy on WiFi and dispatched it quite easily (with a bit of flinchax ;)).
Was something like...
Kabutops used Rock Slide
Manaphy flinched
Kabutops used Rock Slide
Manaphy used Tail Glow
Kabutops used Rock Slide
Woop Woop!
I've read the whole thread, but what hasn't been touched upon is how utterly average Manaphy becomes under the effects of the new and improved Taunt.
Put simply, Manaphy needs to set up to be dangerous.
When Manaphy comes out against something it can't OHKO off the bat, then it's fairly safe to anticipate a Tail Glow, Substitute or a Rain Dance. After Taunt, Manaphy's options are a bit pitiful. Water types can rarely achieve great type coverage, and although Grass Knot is great, it's a free switch in for way too many things.
But what can outspeed him, Taunt him, and then pose an immediate threat?
Well...lets see:
Alakazam...120 base speed, massive Special Attack and access to Calm Mind and Energy Ball should be able to stress out Manaphy if you invest enough SpDef EV's.
Gengar...110 speed, massive Special Attack and Thunderbolt. Lack of Calm Mind/Special Defense makes it an inferior option to Alakazam. Would be better of just Destiny Bond-ing the sod. ^_^
Gyarados...would be a great candidate for the job, with massive Special Defence and HP, plus a Surf resistance. Poor speed is a problem, but if he can catch one of the bulkier, slower Manaphy's then you have an awesome opening to Dragon Dance and sweep.
A few others that, although not neccesarilly sturdy enough or strong enough to damage Manaphy can get the Taunt in to open it up...something like:
Zangoose used Taunt
Manaphy can't use Tail Glow after the Taunt
Lee withdrew Zangoose
Lee sent out Gardevoir
Manaphy used Surf
Then begin Calm Minding or whatever.
Obviously it's not always as easy as having your Taunter against Manaphy first turn. But there's still openings...i.e Manaphy comes out and kills Infernape outright to avoid Close Combat, then you bring out the Taunter.
Not the greatest way of stopping him, but it hasn't been mentioned and I feel it has some serious merit.
But should it be uber? Well...it's too hard to say. I think people can start to underestimate the promise of 100 stats across the board. The fact that it can be fast, powerful and still maintain some bulky water qualities at the same time would make it at least top tier standard.
I'm gonna lean towards "non-uber," but I'm happy to assist in testing the little dude until we can confirm anything.