I'm thinking that the best set would be a four attack set. Something along the lines of:
Shaymin-S @ Life Orb/Yahe Berry
Ability: Serene Grace
EVs: 252 SAtk /252 Spd/4 HP
Timid nature (+Spd, -Atk)
- Seed Flare
- Air Slash
- Earth Power
- Hidden Power [Ice]/Hidden Power [Fire]
Only real counters I can think of are: (Calcs with Life Orb)
Regice (252 HP/ 0 SDef; Calm) takes only 32%-38% from Seed Flare, so it has a small chance of 2HKOing with Stealth Rocks. Ice Beam easily OHKOs it. Though, if it does switch in to a Seed Flare, Skymin can Flinchax it with Air Slash, and then finish it. Yache Varients will always beat it though, 3HKOing with Seed Flare
Registeel (252 HP/200 SDef; Neutral Nature) takes 40%-48% from Earth Power, so Shaymin can't 2HKO. Ice Punch needs a lot of EV investment to finish Shaymin off before he can KO Registeel. Life Orb will finish Shaymin off though. Yache varients will beat it though, 3HKoing with Earth Power.
Bronzong (252 HP/184 SDef; Neutral Nature) cannnot be 2HKO'd by Seed Flare after the SDef drop. It does 26%-31% first time and 52%-63% the second. If Shaymin is running HP Fire then it will KO after an SDef drop. If it doesn't have HP Fire, then Bronzong can put it to sleep or it has a chance to OHKO with Gyro Ball. It does 90%-100%. Life Orb will KO it, but Yache varients have a chance to keep launching Seed Flare untill it Kos. Usually a 3HKO, but it only survives if Stealth Rocks wasn't down and he Seed Flared, and there was an SDef drop.
Crobat (144 HP/112 Atk/252 Spd; Jolly [Enough Atk to OHKO with Brave Bird]) can siwtch in on anything, though switching in on HP Ice while Stealth Rocks is out has a chance to KO. (68%-77%) Shaymin can't really do much else to it though, before it OHKOs with Brave Bird or puts Shaymin to sleep.
All other base 130 mons(and higher) are OHKO'd by Seed Flare on the switch by Life Orb sets, and OHKO'd with SR support by the Yache set.
Thats all I can think of. Notice that all (Except Crobat) are beaten by SubSeeder, and both Regi's lose to Yache version, and none can switch in safely to a Specs version, provided the Shaymin user predicts right. Also only Crobat has access to a healing move, so the Regi's and Bronzong can only switch in once, unless they have Wish support. Shaymin can also run Psychic if it wants to ruining Crobat's switch in.