Glad to see so many suggestions already! There are just some few things I'd like to clear up first. Our definition of checks and counters in this game does in fact not include when being "haxed", but I think it is important to assume that Shaymin will decrease your stats with Seed Flare and at least make you flinch once, because the chances are way higher than the regular "hax" one might encounter elsewhere. I'd say, everything that has a more than 50% chance of happening is not hax, and should be included at least once. You should also consider what happens if you encounter the SubSeed variant more in detail, compared to only assume he uses attacks on you, when he obviously try to set up Seeds and sub stall you and eventually go for either flinch hax or his strongest move, and after that you'll give a sort of detailed description as of how your check beats Shaymin and how safe it is to use to beat Shamyin. Note that if you are faster, a lot of this is not very relevant.
Next up is Soul Dew mechanics. Soul Dew ≠ A Calm Mind boost. This is something many just think because the Soul Dew grants you a 50% boost in both SpD and SpA on the Latis, which is in fact the same boost 1 Calm Mind would give. BUT, when you start doing more than 1 Calm Mind, you stats doesn't continue to boost with 50%, but the boost from Soul Dew still does. After 1 CM, you'll go from a 1.0 boost to a 1.5 boost (50% more), from there it it gets to 2.0 (which 33% more) and then to 2.5 (which is 25% more)... se the pattern? The Calm Mind boost gets smaller each time, but the Soul Dew boost is universal, it will ALWAYS boost your SpD and SpA with 50%. A Lati w/ Soul Dew after 1 Calm Mind will have a 2.25 damage multiplier because it is a 50% boost from a CM + the universal 50% from the Soul Dew, which is significantly better than the +2 CM which only gives a damage multiplier of 2. In the example of Latias after getting her stats lowered by Seed Flare, it is incorrect to assume that she only is at -1 because of Soul Dew.
TL;DR (about Soul Dew): When calcing stuff like that, give the a Assault Vest when calcing defensive capabilities and use Choice Specs when doing offensive ones, that will always be correct, if you combine it with the stats that should be lowered.
I wasn't sure if I should include HP Fire or not, but I can see HP Rock being more useful (even tho none of those would be worse than Healing Wish team support/synergy-wise), so I'll put it there instead of HP Fire and mention Healing Wish. Also, I was thinking about doing Dialga this week, but delayed it because I wasn't entirely sure what set he should have; LO 4 attacks Dialga, Standard Dialga with Toxic + SR that beats the common defoggers, a mix of both, or both at the same time? (Thinking about doing both at the same time, but I'd be glad to get some thoughts on this).