how does Cresselia counter it at all? Psycho Shifting a Burn? Keep in mind Moonlight has 8 PP, and in Sandstream only heals 25%. Also with Torment it wont be able to use it that often.
Oh and in regards to Substitute I can explain how Substitute doesn't change anything if they switch into Toxic Spikes:
Same goes for Flygon (Claw Sharpen set) and Empoleon (Agility Torrent set) that use Life Orb, and with Torment any of the "counters" you listed that have a Choice set can be Struggled to death since the new Gen V mechanics makes Struggle deal 25% damage to the user which happens every other turn (Scizor, Metagross, etc.).
This means if Probopass wanted to KO it, the foe would be Pain Split by 50% each turn (Scizor with Choice Banded Bullet Punch loses 50% Turn 1, then Turn 2 loses another 50% making it at 25%, and to be safe it does it again and loses another 50% making it 12.5% incase Scizor has a Leftovers+1 number for HP; don't worry at 0 HP EVs Scizor at 12.5% has 35 HP, more than enough to heal Probopass to full HP).
Then Probopass uses Torment and survives with 1 HP due to Sturdy, and Protects the next turn it attacks (not the Struggle turn). Scizor is forced to switch out or Struggle to death, at which point Probopass can Pain Split the incoming Pokemon on the switch and heal back-up to 100%, or let Scizor's Struggle to KO itself and make it a double KO. Regardless, Probopass is not countered, it is simply equally matched; at best. Oh, and if you wanted to preserve it (like Baton Pass it Wish/Leech Seed), then you could switch out Probopass while Scizor KOs itself.
Oh and in regards to Substitute I can explain how Substitute doesn't change anything if they switch into Toxic Spikes:
For example, if you're using this set you will almost certainly have SR and Sandstorm, hopefully Toxic Spikes as well.
So opponent switches in, takes 25% from SS+SR+TS (More if they're SR weak). Next turn they set up Sub, that+SS+TS = 44%. They attack you next turn, only to lose 25% as you Protect. So they'll be left on 6%. Even with Leftovers they're on 25%, and Toxic Spikes will kill them next turn, which they'll be using to reduce your Probopass' HP to 1, surviving with Sturdy. So Probopass still wins.
Obviously something with a typing like Flygon is OK, as it's immune to T Spikes and SS, but other Sub users would be hard pressed to beat this thing.
Of course it can be beaten with prediction but it could stall pretty well if played smartly, and on that last turn you could just switch out Probopass as it has already done its job.
Also keep in mind that while Flying, Levitate, Poison, Steel types are Immune to Toxic Spikes, Probopass can still use Pain Split on ones without Substitute / Taunt. And ones like Gengar whom take Sandstream damage, Probpass can simply Protect + Pain Split stall for Sandstream damage.
As for Landorus, it doesn't pack Taunt in its sets, and can pack Life Orb on its Rock Polish/Swords Dance sets (making a KO possible) since it lacks recovery. So it is a * at best if packing Leftovers over Life Orb on the Swords Dance set. The reason being that Landorus basically gets Pain Splitted as Life Orb damage racks up.(i.e. say Pain Split+Sub Gengar switches in while Probopass uses Pain Split. )
Gengar takes 56.25% damage (50% + Sandstream).
Probopass uses Pain Split again as Gengar uses Substitute causing Pain Split to fail, but works as an insurance incase Gengar attacks; Gengar takes 31.25% damage from Substitute and Sandstream.
Probopass uses Protect and Gengar takes 6.25% damage, leaving Gengar at 6.25% (a Sandstream KO next turn).
Switch out Probopass and Gengar dies either to Sandstream, or by Life Orb if it tries to attack, (if you predict Gengar will use Pain Split then keep Probopass in). If Probopass is the last Pokemon left, Probopass will take the hit, survive at 1 HP due to Sturdy and Gengar still dies from Sandstream/Life Orb.
Same goes for Flygon (Claw Sharpen set) and Empoleon (Agility Torrent set) that use Life Orb, and with Torment any of the "counters" you listed that have a Choice set can be Struggled to death since the new Gen V mechanics makes Struggle deal 25% damage to the user which happens every other turn (Scizor, Metagross, etc.).
This means if Probopass wanted to KO it, the foe would be Pain Split by 50% each turn (Scizor with Choice Banded Bullet Punch loses 50% Turn 1, then Turn 2 loses another 50% making it at 25%, and to be safe it does it again and loses another 50% making it 12.5% incase Scizor has a Leftovers+1 number for HP; don't worry at 0 HP EVs Scizor at 12.5% has 35 HP, more than enough to heal Probopass to full HP).
Then Probopass uses Torment and survives with 1 HP due to Sturdy, and Protects the next turn it attacks (not the Struggle turn). Scizor is forced to switch out or Struggle to death, at which point Probopass can Pain Split the incoming Pokemon on the switch and heal back-up to 100%, or let Scizor's Struggle to KO itself and make it a double KO. Regardless, Probopass is not countered, it is simply equally matched; at best. Oh, and if you wanted to preserve it (like Baton Pass it Wish/Leech Seed), then you could switch out Probopass while Scizor KOs itself.