I can see why manaphy is in Ubers because it is so powerful, but specs jolteon's thunderbolt does 82-97% damage to a MAX HP/SDef positive SDef nature manaphy, and then you can just priority move it if manaphy kills jolt (Thunder is guaranteed OHKO, if it matters)
More damage calcs (using standard spreads to same manaphy ^):
0CM Raikou T-bolt: 68-80%
1CM Raikou T-bolt: 101-120%
CB Metagross Bullet Punch: 13-15% (eh, ~94% KO w/ Jolt)
Specs Deoxys-E T-bolt: 51-58%
Standard Gengar T-bolt: 37-44% (Timid Scarf same %)
Modest Scarf Gar T-bolt: 41-48%
Specs Gar T-bolt: 56-66%
Remember, this is to MAX HP/SDEF +SDEF nature Manaphy!
A lot of their effectiveness will depend on how well they can handle the combination of rain/tailglow boosted Surfs, Grass Knot, or Ice Beam (or hidden power..). With Manaphy devoting everything to defenses, its offensive fire power is toned down.. but only a bit.
On the before mentioned defensive Manaphy Sleep Talking set, I think having Manaphy setup its own Rain Dance takes away from its versatility attacking wise. It leaves itself open to the like of Toxicroak, and Grass Pokemon if it fails to carry Ice Beams.. and struggles against against other waters if it lacks HP Electric/Grass Knot.