Seriously, here are my thoughts on the suspects so far:
Latias: The Choice Specs set is obviously its most powerful, and in my opinion, qualifies it for Uber status. I've seen most people use ScarfTar to beat it, which really only wins 50% of the time. Other attempts at counters I've seen are Specially Defensive Jirachi and Metagross, which, are ok but Latias can always switch out and continue firing off Draco Meteors.
Manaphy: I've been using Scarf Manaphy for most of my laddering so far, which has been doing great. However, the Tail Glow set is still very powerful and really sweeps through teams when played in the right hands. Both of my teams have a way to handle it (Specs Latias, DDWacanGyara lure, and Blissey), but outside of that, little else stops it. I'd go as far as to say the mono-attacking Manaphy is also broken since little stops it after it racks up sufficient Calm Minds, and it doesn't suffer from two turns of resting like Suicune. The best way I've been able to beat it is by Tricking it Choice Specs, but that isn't very reliable.
For Latias, just to note, Jirachi and Metagross can still act as counters for it. The CM + Wish Jirachi can use Latias as setup bait if it comes in on something that isn't Trick. A Specs Surf only does 34.2% - 40.3%, meaning that Jirachi can just come in, Wish, Calm Mind, and start setting up. Latias is also in a lot of trouble against the Scarf set (which I assume is the thing that's been haxing the hell out of you). For Metagross, they've been running Pursuit more often, so it's not quite that easy to just switch out and come back in.
Also, I have a few comments about what you said about Manaphy. You say that "the Tail Glow set is still very powerful and really sweeps through teams when played in the right hands", but that's just it. It sweeps through teams "
when played in the right hands". Not everyone who plays suspect is an absolute guru at playing pokemon, and this is something I've been thinking about for a while. While they may not be horrible, if the average player is genuinely having trouble sweeping with the Tail Glow set, even with a good team, then as far as I'm concerned, it's not uber. A ridiculously good player can make even a weaker pokemon sweep, because they know very well how to get rid of that pokemon's counters, and the best times to switch it in, while an average player (read: not a horrible one) may not. I personally don't think this is a broken set, because it's still really hard to get a clean sweep if there are any Scarf users or pokemon over 328 Speed on the opposing team, which honestly aren't hard to come by. While it seems very hard to counter on paper, this honestly just isn't the way it works out if faster pokemon aren't gone. They discourage it from Tail Glowing, and make it hard to sweep, so therefore they must be removed before Manaphy can sweep. According to the offensive characteristic, it should not require this much effort to sweep to qualify for uber, so I don't believe it fits it.
About the mono-attacking set, I highly disagree with you on that one being a broken set. So many things are carrying Electric attacks in this ladder, and there's a lot of U-turning happening as well. When I used it, I found it ridiculously hard to set the mono-attacking Manaphy up, because not only is there Water Absorbers such as Vaporeon, or a 4x resist like Kingdra that you have to get rid of, but this variant uses so much HP and Defense EVs that it's so slow and weak, and getting something like 4 Calm Minds to sweep is not easy with how offensive this ladder is. If TTar, Hippowdon, or Abomasnow come in on the Rest (or in Abomasnow's case, anything that isn't Rain Dance), Manaphy's sweep is in danger of ending, if it even began at all. I don't believe this would fit the offensive characteristic either, because it needs to get rid of any weather changers, get rid of Water Absorbers, any Trickers will make your life trouble, and stuff like opposing Kingdra will thank you for doubling its Speed while taking next to nothing from your attacks. I personally thought this set was better when Garchomp was still around, because he could at least help by getting rid of Electrics, also absorbing Trick pretty nicely.
EDIT: @nightmarez:
hmmm I'm gonna go do some damage calcs on a haban berry CMmanaphy
This doesn't even work. The type-resist berries only work if you're weak against the attack (with the exception of the Normal-resist berry).