Keep in mind that as I'm writing this from the perspective of someone who sees Vaporeon as THE #1 most threatening pokemon and Suicune as #2. People seriously do not understand how far bulky waters shape the game and keep offensive teams in line. In the advent of mix-attacking wall breakers like infernape and salamence as well as guess-the-set pokes like Luke and water-based dragon dancers like Kingdra and Gyarados, it's not SkarmBliss that stops offensive pokes from running amuk-- it's the combined front of vaporeon, suicune, swamert, starmie and tentacruel.
Bulky waters are near-integral to the balance of the metagame, but are also a pokemon group that goes largely unchecked. While they are not walls that last the whole game, they are tanks that are bound to have a huge impact on the shape of the early game before they go down. If you play an offensive team in DP, your #1 priority in early game is: kill the bulky water, even if it costs you 1-2 members of your team.
Water has 2 weaknesses that are very hard to abuse. Grass is one of the less used attacking types, and grass pokemon have to fear ice beam. Electric is terrible as a main STAB as it is immuned by the ever-present ground (and swampy lols). The top electric types of the game rarely go to all-out-sweeper sets (zappy and rotom are usually tankish). Both electric and grass are popular as secondary attacks on pokemon without STAB, but without stab bulky waters have a decent time shrugging it off.
Water also has amazing nuetral coverage, resisted only by dragon, grass and water. Of course water v. water just means more water types around (and leads to headaches near that of blissey v. cresselia) and both dragon and grass are weak to ice (which of course every water type can pack, thanks GF). Throw in a grass/electric attack and you have perfect coverage, though many water types have success just by spamming their stab alone. Sleep Talk Gyara or Suicune with Waterfall as their only attack are surprisingly powerful for example.
Pure Water is one of the most powerful and offensively/defensively balanced types a pokemon can have.
With that in mind, Manaphy could be the water type to end all water types. 100 in every base stat is very good, and compliments water types balanced nature.
It's 1 tier weaker than suicune in both defenses. You guys all know how bulky celebi and jirachi are (and they have much more easily abused weaknesses). As a quick comparison, this means it is 3 tiers above Vappy on defense and 1 tier below on special defense (3 tiers is the difference between Empoleon and Aerodactyle btw). It's also roughly the same tier (on both sides) as Tentacruel's Special Defense. Goes without saying that it is a notch tougher than swampert on either front.
100 speed tier is nothing to scoff at either. The ability to go on the offensive on either side of the spectrum with decent power is also troubling.
Even before looking at its traits or any of its moves, its clear that we are looking at a definite top tier pokemon. For the most part though, I'd say that
swampy has SR!
Vappy has Wish!
Tentacruel has Spin, Knock Off and Toxic Spikes!
I'm not going to lie that lacking a truly intimidating set up move is definitely one of its weak points, as well as any really reliable recovery. However that never stopped sleep-talk suicune. Imagine a slightly less bulky suicune with Hydro-Rest and Nasty Plot. That's Manaphy.
It's not like it's totally screwed on the support-move side either. Double Screen Manaphy anyone? :P