It's Shaymin. Manaphy is clearly obtainable in another game, and not through any nintendo event, to add to that. All of Mew (excluding the newly introduced Pokemon Ranch), Celebi, Jirachi and Shaymin all needed nintendo events to unlock them.
In addition, Manaphy has another form, well, not a form, but a spawn. This removes it from the previously stated category because this is an abnormality that the MC and J don't have. As far as power and stats go, that shouldn't be a concern, because the question is whether or not it belongs in the cute, super-legendary team in a formulaic pattern as the other three did. Also, with the news of a second Manaphy in the next Pokemon Ranch, this makes it even less likely to be seen as so rare.
You could argue that it's Manaphy simply by the fact that it retains similar proportions and shapes to the other three, but then, you'd have to consider Mesprit, Uxie and Azelf. Just because the body shape emulates the others doesn't mean they were put into that pattern.
The only major difference with Shaymin, as opposed to the other three, is that it's not at the end of the numbering sequence for that series, Arceus is. Truly, if we were going with this logic alone, Arceus would be the feesable choice. But, seeing as we've narrowed it to a "cute" pokemon, the answer is obvious.
Manaphy is much more obtainable and retains breeding abilities that are ultimately its own. For the reasons and more, I say Shaymin is the true super-rare, cute legendary for the fourth series. ;492;
