You argue Manaphy is not uber because Calm Mind Blissey is not bad? How does that make sense?
Its because no one uses it, and therefore, concluding that its uber. Just because only one pokemon counters it, doesn't really mean it's going to ubers. If an uber is something that debalances the game, I don't see how Manaphy makes a debalance when something right there is available for use that can counter it, and especially when that thing also does other things besides countering Manaphy. If every team is pretty much forced to use some sort of special defense, isn't it the best option to maximize that capability whenever your team needs it?
Of course, not everyone wants Blissey. They think it's uncreative blah blah, but then, it all comes down to this: A successful team must have either a centric strategy, a balance between offense and defense, or both. When it comes down to special walling, you must choose carefully. Snorlax does not have a reliable method of recovery, Cresselia is weak to SHadow Ball and its recovery move is limited AND hampered by Sandstorm. Also, it doesn't have Seismic Toss. Also using Cresselia as your special wall also means you can't use it to counter Garchomp. Empoleon is a no.
Now, when it all comes down to bliss, you must choose again the sets. While you say Manaphy forces to use a different Blissey set, it is not like if the standard set does the real job of a Blissey any better than the Calm Minder one. The standard set itself is a bigger set up bait than the Calm Mind one, and get stalled easier (Skarmory sets up Spikes all over you, Zapdos Roosts on your Tosses/Beams, etc). While the standard Bliss carries a status move, it's really pretty predictable and can be easily handled, thus leaving you with practically one real choice even before Manaphy is considered, although I wonder why people use their standard Bliss and say it counters Zapdos in their RMTs (I believe). Just because it limits the option doesn't mean its uber if that certain set can easily fit in your team and not overspecialize on that particular thing at the same time, as CMBliss does a few more things than just cover up Manaphy which the standard Bliss can't. Yeah, I understand Blissey can be a cleric too, but the D/P metagame is too fast paced for such option
So with that in mind, Manaphy should no longer be the biggest worry in people's teams, and it also solves those who want to use them.
Also, Mekkah. Is that really your Friend Code?