Skymin counters
POSSIBLE COUNTERS:
Zapdos
Crobat*^
Registeel+
Regice+
Dragonite*
Blissey
Bronzong
Italicized: Slightly less popular.
*: Cannot be flinched due to Inner Focus; 4x resist against GRASS.
+: Has Clear Body to prevent Stat Losses.
^: Faster than Sky Shaymin.
Feel free to discuss anything related to Skymin.
Jrrrrrrr's post stated much that I missed so I'll post it here as a quote:
This post is dedicated to discussing the effectiveness of Skymin's counters. SR is taken into account with all counters, as it is likely to be in play due to Rapid Spin being less common and Rotom's forms proving to be common and effective anti-spinners.
Crobat against Specs Skymin - read blasphmey1's post.
Crobat against Subseed Skymin - reliable, because Crobat can swap in as Skymin uses Air Slash or Sub, and Crobat can survive an Air Slash with SR damage and OHKO back with Brave Bird. But Brave Bird recoil will kill Crobat in such a case.
A Calm Zapdos with max Hlth and SpcDef EVs survives two Specs Skymin Seed Flares, with a SpcDef Drop from the first hit,
if SR is not in play. Zapdos is not a reliable Specs Skymin counter.
Zapdos with Leftovers or Scarf should be comfortable against Subseed Skymin unless it gets flinched by Air Slash (not tested). Zapdos definitely works if it swaps in when Skymin does not have a sub up.
Registeel can take Skymin's hits comfortably. However, Magnezone can be sent in on him (and Registeel will probably not Earthquake if Magnezone has not been revealed in the battle yet). Magnezone beats Registeel after Magnet Rising if he does not get hit by Thunderwave. If Registeel has Rest and Sleep Talk, after sleeping, he is not able to reliably counter Skymin until he wakes up (Magnezone can swap out to something threating like Mamoswine or SD LO Scizor with Brick Break/Superpower).
Bronzong is a worse Registeel but with Hypnosis instead of Thunderwave. Furthermore, a Bronzong is very unlikely to have both HP Ice and Earthquake. Gyro Ball gets stalled out by Subseed Skymin.
Blissey - read previous posts by me and IggyBot.
Dragonite with no SpcDef or Hlth EVs always gets 2HOKed by Specs Air Slash, with or without SR damage. Scarfnite can swap in and survive any hit but HP Ice and OHKO Skymin with no Hlth or SpcDef Evs with Ice Beam and no SpcAtt EVs, neutral nature. Dragonite with SpcAtt EVs can OHKO any Skymin with Ice Beam. Outrage on 252 Att EVs, Jolly Scarfnite (Adamant nite is slower than Timid Skymin) does 256-301 (278.88 average) with Outrage. Skymin needs SR damage to be OHKOed (which may be healed off by Leftovers).
In short, Scarfnite needs Ice Beam to be a reliable Skymin counter (and a speed boosting nature with Spc Att EVs)
Regice should work as long as Air Slash does not flinch on any Skymin (not tested).
Timid Scarfran can take any of Skymin's hits apart from Earth Power. He does not fear Magnezone. He is a reliable counter, unless the Skymin has a Sub up and knows Earthpower (which is unlikely).
Skarmory with SpcDef and Hlth EVs can tank Specs Skymin's attacks, even with a SpcDef drop (Impish Skarm with 252 SpcDef EVs, takes 69-81 (75.05 average) from Specs Seed Flare) and an Air Slash flinch and be a threat with Drill Peck and Brave Bird, but he dies horribly to Magnezone unless he has Shed Shell. Without the Shed Shell, he can only Whirlwind Subseed Skymin away, as without the Leftovers, Leech Seed wears him down too much (Brave Bird recoil wears him down too much even if Skarm has Leftovers). This assumes that Skarm swaps in to Skymin as she uses Sub. So Skarm only reliably counters Specs Skymin with a Shed Shell. He can only reliably phaze Subseed Skymin.
To conclude, Timid Scarfran, Regice (probably) and Scarfnite with Ice Beam (who may get worn done by repeated switching with SR damage) are the only reliable Skymin counters (both Specs and Subseed) (assuming the Skymin has a Magnezone ally).
If one of these is not on your team, you may have to sacrifice a pokemon in order to Ice Shard Skymin (who, shown by how hard it is to counter Skymin, does not need a Yache Berry, unlike Garchomp. But if she does have one, the Ice Shard may not KO.)