A Choice Scarf enables Shaymin-S to become both a great revenge killer and a decent lead. It's also arguably the best offensive answer to Rock Polish Groudon, as it is immune to Earthquake, and it can outrun most Groudon even after a Rock Polish and OHKO it with its powerful STAB Seed Flare. As a lead, it should try for an Air Slash flinch against Deoxys-A and Deoxys-S leads, which will usually prevent them from setting up entry hazards, and it easily beats Groudon leads who don't invest heavily in Special Defense.
Both of Shaymin-S's STABs allow it to get out of many tough situations thanks to Seed Flare's 68% overall Special Defense drop rate, as well as Air Slash's 57% overall flinch rate and neutrality against most Pokemon in the Uber environment. Earth Power 2HKOes most Steel-type switch-ins, though specially defensive Dialga will survive two Earth Powers, usually even after a Special Defense drop. Hidden Power Ice allows Shaymin-S to revenge kill Garchomp, opposing Shaymin-S, and Dragon Dance Rayquaza lacking Extreme Speed.
Non-lead Shaymin-S should have a Modest nature to guarantee Seed Flare's OHKO on faster variants of Kyogre with Stealth Rock damage. The only somewhat common Pokemon in Ubers who will outspeed Modest Shaymin-S are Timid Choice Scarf Darkrai, opposing Shaymin-S, and Mewtwo. When used as a lead, Shaymin-S should be Timid so that it can outspeed the aforementioned Darkrai, another common lead.
Leaf Storm is an option to use in place of Seed Flare with a Modest nature, which OHKOes both max HP Kyogre and 4 HP / 0 SpD Darkrai after Stealth Rock damage. However, this leaves Shaymin-S vulnerable to Calm Mind users like Latias and Mewtwo, and Leaf Storm lacks the Special Defense lowering effect of Seed Flare. Thus, it should only be used if Shaymin-S's team really needs the KOs that Leaf Storm provides. Don't use Leaf Storm with a Timid nature, as the only benefit to doing so is gaining an OHKO on 4 HP / 0 SpD Kyogre after Stealth Rock.
Generally, Choice Scarf Shaymin-S's biggest foes resist its STABs or have extremely high special bulk. Scizor and Dialga can heavily dent Shaymin-S with most of their attacks, with Choice Band Scizor dealing at least 53% with Pursuit, which is potentially fatal with Stealth Rock in play, while Dialga can set up on Shaymin-S with Bulk Up. Lugia, opposing Shaymin-S, Rayquaza, Ho-Oh, Latios, and Latias can switch into Seed Flare and Earth Power and either threaten Shaymin-S immediately or set up. The massive defensive stats of Giratina, specially defensive Skarmory, and Blissey allow them to shrug off Shaymin-S's assaults to cripple it in various ways (e.g. status, phazing, PP stalling), as long as Seed Flare doesn't net too many Special Defense drops. Giratina-O is a more offensive check that can pick off a weakened Shaymin-S with Shadow Sneak. Finally, Wobbuffet can easily trap and revenge kill Choice Scarf Shaymin-S with Mirror Coat.
In terms of teammates, mixed variants of Dialga, Palkia, and Rayquaza can lure in most of Shaymin-S's defensive checks. For a more threatening approach, Darkrai and Calm Mind Mewtwo can set up on and crush Shaymin-S's checks quite well. Alternatively, Wobbuffet can trap and KO many of Shaymin-S's checks. For Mixed Dialga, it's best to revenge kill it via Pokemon like Garchomp and Lucario. Good defensive partners include Kyogre, Groudon, Jirachi, and Blissey.
Something to note about leading with Choice Scarf Shaymin-S is that it often relies on Air Slash's flinch rate to beat other leads such as Darkrai, so having a Sleep Talker waiting in the wings such as Kyogre is advisable. Hidden Power Fire is a viable option on this set to destroy Scizor leads and Forretress or Skarmory switch-ins. However, it requires Shaymin-S to lower its Speed IV to 30, meaning that opposing Choice Scarf Shaymin-S will beat it.
There are also several leads that almost always beat Shaymin-S: Choice Scarf Mewtwo outspeeds Shaymin-S and OHKOs with Ice Beam, while 252 HP Kyogre, Dialga, and Tyranitar can survive one of Shaymin-S's attacks and OHKO in retaliation. Scizor leads trouble Shaymin-S that lack Hidden Power Fire, 3HKOing with Bullet Punch. An allied Blissey can easily wall lead Kyogre, Dialga, and Mewtwo, while Groudon can switch into Tyranitar and Scizor and severely damage or OHKO them with Earthquake or a Fire-type attack. Although Draco Meteor will do a huge amount of damage to Groudon, STAB Earthquake will often scare Dialga off as well. While Palkia and Latias can destroy Kyogre, several lead Kyogre carry Thunder Wave to take advantage of these switch-ins. A Dialga of your own can switch into Mewtwo, Kyogre, and Scizor, and threaten them with Draco Meteor, Thunder, and Fire Blast respectively.