The top two leads in the Uber metagame are, by far, Deoxys-S and Scarf Darkrai. I wanted to create a lead that can take on both of these two. I have extensively tested this, and I have found it is very effective at neutralizing these two leads, as well as some other common leads.
Analysis: http://www.smogon.com/dp/pokemon/mewtwo
[EDIT] 28/12/2008 - Removing Taunt as a main option, and adding information about stealing Latias' Soul Dew.
[SET]
Name: Scarf Lead
Move 1: Focus Blast
Move 3: Shadow Ball
Move 2: Ice Beam / Trick
Move 4: Selfdestruct
Item: Choice Scarf
Nature: Hasty
EVs: 40 Atk / 252 SpA / 216 Spe
[SET COMMENTS]
<p>This set aims to tackle many common leads. No Pokémon resists both Focus Blast and Shadow Ball. With a Choice Scarf and the given EVs, Mewtwo has just enough to speed to outrun Timid Scarf Darkrai, and hence anything else you are likely to encounter in Ubers. Mewtwo threatens a OHKO with Focus Blast. Aura Sphere is not mentioned, as it only has a 15.38% chance of a OHKO. It may seem risky to rely on Focus Blast’s shaky accuracy, but in case of a miss, Mewtwo will always survive a Timid Scarf Darkrai’s Dark Pulse. Focus Blast 2HKOs all variants of Dialga as well, with only Bulk Up Dialga having a slight chance of survival with Leftovers recovery (Bulk Up Dialga takes 52.97% - 62.87%).</p>
<p>Shadow Ball hits many Ubers super effective, 2HKOing Deoxys-S, Mewtwo and Mew. Taunt is an option over Shadow Ball, but only if you have a Pokémon with Focus Sash on your team. It is the only way to prevent Deoxys-S from setting up Stealth Rock. After using Taunt, the opposing Deoxys-S should swap out, as you swap to your own Focus Sash user with your Focus Sash inact. This works great with your own Deoxys-S. However, this does not stop the opposing Deoxys-S from coming back into play later and setting up whatever it wants.</p>
<p>Selfdestruct is a must on such a speedy pokemon, hitting many of the ubers on their lower defense stat. Selfdestruct is Mewtwo’s only way of dealing with some leads, mainly Kyogre. It OHKOs 4 HP / 0 Def neutral nature Kyogre, Rayquaza and Palkia. 4 HP / 0 Def Timid Mewtwo has a 99.44% of being OHKOed, and 4 HP / 252 Def Calm Blissey has a 98.93% chance of being OHKOed. These damage calculations exclude Stealth Rock damage.</p>
<p>Ice Beam makes a good choice on such a fast Pokemon. It provides very good coverage in Ubers, hitting many of the Uber Dragons super effective, as well as Groudon, and even hitting Rayquaza and Garchomp for x4 damage. On that topic, Mewtwo is an ideal revenge killer of a Dragon Dance boosted Rayquaza, but unfortunately, Mewtwo cannot swap into a Life Orb Outrage, boosted or not. Ice Beam always 2HKOs 252 HP / 4 SDef Groudon, and Mewtwo is never OHKOed by a Groudon’s Earthquake without an item boost, even if Stealth Rock is in a play. A Life Orb Adamant Groudon’s Earthquake only OHKOs Mewtwo 28.21% of the time if Stealth Rock is not in play. The other option over Ice Beam is Trick, which can be used to cripple walls like Blissey or Lati@s. In fact, after stealing Latias' Soul Dew, Shadow Ball has a 87.51% chance to 2HKO the standard set (Timid 112 HP / 0 SDef) without Stealth Rock damage, while in turn, she will only have a 19.79% chance to 2HKO with an unboosted Dragon Pulse if Stealth is in play. Trick also works effectively with a Pursuit user on your team. After using Trick on these Pokémon, they will hopefully be locked onto a move that will enable your Pursuit user to swap in with little risk, enabling you to use Pursuit as they swap out. Obviously, don’t use Trick with Taunt, as Focus Blast has very limited coverage in a metagame full of Psychic Pokémon.</p>
<p>Hasty is the preferred nature. This allows Mewtwo to outspeed Timid Scarf Darkrai and most Groudon after a Rock Polish boost. 252 Special Attack is self-explanatory, powering up Focus Blast, Shadow Ball and Ice Beam. The rest goes into Attack to power up Selfdestruct. 40 Attack guarantees a OHKO with Selfdestruct on Kyogre, Rayquaza and Palkia.</p>
Analysis: http://www.smogon.com/dp/pokemon/mewtwo
[EDIT] 28/12/2008 - Removing Taunt as a main option, and adding information about stealing Latias' Soul Dew.
[SET]
Name: Scarf Lead
Move 1: Focus Blast
Move 3: Shadow Ball
Move 2: Ice Beam / Trick
Move 4: Selfdestruct
Item: Choice Scarf
Nature: Hasty
EVs: 40 Atk / 252 SpA / 216 Spe
[SET COMMENTS]
<p>This set aims to tackle many common leads. No Pokémon resists both Focus Blast and Shadow Ball. With a Choice Scarf and the given EVs, Mewtwo has just enough to speed to outrun Timid Scarf Darkrai, and hence anything else you are likely to encounter in Ubers. Mewtwo threatens a OHKO with Focus Blast. Aura Sphere is not mentioned, as it only has a 15.38% chance of a OHKO. It may seem risky to rely on Focus Blast’s shaky accuracy, but in case of a miss, Mewtwo will always survive a Timid Scarf Darkrai’s Dark Pulse. Focus Blast 2HKOs all variants of Dialga as well, with only Bulk Up Dialga having a slight chance of survival with Leftovers recovery (Bulk Up Dialga takes 52.97% - 62.87%).</p>
<p>Shadow Ball hits many Ubers super effective, 2HKOing Deoxys-S, Mewtwo and Mew. Taunt is an option over Shadow Ball, but only if you have a Pokémon with Focus Sash on your team. It is the only way to prevent Deoxys-S from setting up Stealth Rock. After using Taunt, the opposing Deoxys-S should swap out, as you swap to your own Focus Sash user with your Focus Sash inact. This works great with your own Deoxys-S. However, this does not stop the opposing Deoxys-S from coming back into play later and setting up whatever it wants.</p>
<p>Selfdestruct is a must on such a speedy pokemon, hitting many of the ubers on their lower defense stat. Selfdestruct is Mewtwo’s only way of dealing with some leads, mainly Kyogre. It OHKOs 4 HP / 0 Def neutral nature Kyogre, Rayquaza and Palkia. 4 HP / 0 Def Timid Mewtwo has a 99.44% of being OHKOed, and 4 HP / 252 Def Calm Blissey has a 98.93% chance of being OHKOed. These damage calculations exclude Stealth Rock damage.</p>
<p>Ice Beam makes a good choice on such a fast Pokemon. It provides very good coverage in Ubers, hitting many of the Uber Dragons super effective, as well as Groudon, and even hitting Rayquaza and Garchomp for x4 damage. On that topic, Mewtwo is an ideal revenge killer of a Dragon Dance boosted Rayquaza, but unfortunately, Mewtwo cannot swap into a Life Orb Outrage, boosted or not. Ice Beam always 2HKOs 252 HP / 4 SDef Groudon, and Mewtwo is never OHKOed by a Groudon’s Earthquake without an item boost, even if Stealth Rock is in a play. A Life Orb Adamant Groudon’s Earthquake only OHKOs Mewtwo 28.21% of the time if Stealth Rock is not in play. The other option over Ice Beam is Trick, which can be used to cripple walls like Blissey or Lati@s. In fact, after stealing Latias' Soul Dew, Shadow Ball has a 87.51% chance to 2HKO the standard set (Timid 112 HP / 0 SDef) without Stealth Rock damage, while in turn, she will only have a 19.79% chance to 2HKO with an unboosted Dragon Pulse if Stealth is in play. Trick also works effectively with a Pursuit user on your team. After using Trick on these Pokémon, they will hopefully be locked onto a move that will enable your Pursuit user to swap in with little risk, enabling you to use Pursuit as they swap out. Obviously, don’t use Trick with Taunt, as Focus Blast has very limited coverage in a metagame full of Psychic Pokémon.</p>
<p>Hasty is the preferred nature. This allows Mewtwo to outspeed Timid Scarf Darkrai and most Groudon after a Rock Polish boost. 252 Special Attack is self-explanatory, powering up Focus Blast, Shadow Ball and Ice Beam. The rest goes into Attack to power up Selfdestruct. 40 Attack guarantees a OHKO with Selfdestruct on Kyogre, Rayquaza and Palkia.</p>