I thought Manaphy was more useful in Ubers than out. It has the best health recovery system in the game, courtesy of Kyogre's Drizzle and its own Hydration. STAB Surfs backed by the boost from rain have a heck of a sting on them, it is faster than lots of things in Ubers, it has an excellent and reliable way to boost its stats (thus it can OHKO Kyogre with Grass Knot after a Tail Glow boost, so Kyogre is no threat really), it is versatile enough to do pretty much everything it wants (I'm fairly sure it can run defensive sets with Light Screen and Knock Off or Offensive physical sets with Waterfall and U-turn) it resists the ice attacks that fly pretty much everywhere in Ubers and it can nick the boosts off others with Heart Swap.
It really is a monster. At least, it is in my opinion.
EDIT: Not that it really matters, but wouldn't Ho-oh break up the 'Holy Trinity' that seems to be everywhere currently, of Heatran/Scizor/Skymin?