I am going to dedicate this post to Latios, and some to Shaymin-S. Of course, some of it may be shizz, because I am tired (nonetheless it isn't an excuse).
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Lets look at its counters and checks; Blissey, Jirachi, Registeel, Tyranitar, Metagross, Snorlax, Bronzong, Empoleon, Special Defensive Skarmory, Special Defensive Scizor.
Blissey: Takes Draco Meteors easily, just has to watch out for Trick Specs.
Jirachi: Even variants without HP and SpD EVs take only around 55% from a Specs Draco Meteor. Access to Wish, Ice Punch, Thunder Wave/Body Slam, Iron Head helps Jirachi be one of the top Latios counters in the game outside of Blissey.
Registeel: Non-Special Defensive variants take 39.01%
max, sporting also Ice Punch and Thunder Wave, help it take on Latios. RestTalk versions are even better at walling Latios.
Tyranitar: Special Defensive variants, takes around 45% from a Specs Draco Meteor, lets not forget SpA lowering factor. Pursuit kills Latios easily, but only has to watch out for Surf.
Metagross: Takes around the same amount no HP/Def Jirachi takes when he has max HP from a Specs Draco Meteor. Max HP/SpD (with Adamant) take only around 42%. Still a okay counter nonetheless, and can Pursuit or Meteor Mash Latios to its grave.
Snorlax: Basically takes the same as Metagross from Specs Draco Meteor, and has access to Pursuit, but only does a little. Metagross usually does the job better though.
Bronzong: Standard sets take 40% some, but special ones take 35% some (Specs DM). Gyro Ball deals a hefty amount to Latios due to his high Speed.
Empoleon: Takes about the same as Bronzong, and has Ice Beam, but has to watch out for Thunderbolt.
Special Defensive Skarmory: Just watch out for Thunderbolt...
Special Defensive Scizor: Takes 44% some if Scizor is Careful with max HP/SpD, it counters it I guess. But, having to run those EVs and Nature makes Scizor not as helpful as it once was as its Attack would have lowered in the process.
Heatran can check it as well, just needs to watch out for Surf. And, same with anything else, you can revenge kill with a good amount of Pokemon. Lets not forget that it does take a good amount of damage just switching into somethings like Heatran and Infernape.
Offensive Characteristic
A Pokémon is uber if, in common battle conditions, it is capable of sweeping through a significant portion of teams in the metagame with little effort.
I find this hard to answer with Latios. >.< It does have to worry about Blissey (of course), Steels, Pursuit users, and revenge killers. Some Steels like Jirachi and Registeel can wall it to no end, Pursuit users can kill off Latios easily, and just with everything, a revenge killer can kill of Latios pretty easily (Heatran, Scizor, Mamoswine, Starmie, Gengar, etc). Some teams may have to sacrifice a Pokemon to defeat Latios, but most teams certainly have a Scarf user, or something faster than Latios like SpecsJolt, to kill it off with little effort (definitely if Latios's Speed has dropped). While it is a difficult Pokemon to counter, as with DD Mence, there are ways of defeating it. I still find it hard to answer this if it is Uber or not.
Support Characteristic
A Pokémon is uber if, in common battle conditions, it can consistently set up a situation in which it makes it substantially easier for other pokemon to sweep.
Yeah, Latios fits this with Dual Screen Memento... If only Game Freak never gave Latios Memento, Latios would not fit this as much. :(
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I am getting tired, so I am just going to do the Uber characteristics.
Offensive Characteristic
A Pokémon is uber if, in common battle conditions, it is capable of sweeping through a significant portion of teams in the metagame with little effort.
Flinching and SpD lowering is definitely not a common battle condition, and Shaymin-S has to rely on luck to win the battle, and losing on the flinch rate could mean the entire battle. Lets not forgot a huge handful of Pokemon in OU can take down Shaymin-S quite easily if the flinch rate was not included. It also has a problem switching in sometimes outside of its Ground immunity.
Defensive Characteristic
A Pokémon is uber if, in common battle conditions, it is able to wall and stall out a significant portion of the metagame.
Shaymin-S can stall the metagame greatly with the SubSeed set. But, it has problems with Stealth Rock and sandstorm, which are considered common battle conditions. It can stall, but not wall with huge amount of weaknesses, SR weakness, sandstorm weak, and standard defense stats. Lets not forget this part also; "-it is able to
wall and stall-".
Support Characteristic
A Pokémon is uber if, in common battle conditions, it can consistently set up a situation in which it makes it substantially easier for other pokemon to sweep.
Shaymin-S does not support barely any for its team members, it only weakens the foe, and may defeat a Pokemon, but that is certainly not support. Sometimes Shaymin-S is the one needing support.