Khan Noonien Singh's Advantages
1. Strength
2. Intelligence
3. Recovery/Healing/Resilience
4. Weaponry/Ranged Combat
The boolean gun was a type of large and bulky hand-held directed energy weapon used by Khan Noonien Singh, a former operative of Section 31 of Starfleet. Despite its size, the weapon could be operated with a single hand and was carried with a shoulder strap.
When activated, the boolean gun produced powerful bright streams of energy and a loud roaring noise. The energy streams could slice through and vaporize holes into anything they were targeted at, from personnel to starship hulls.
http://en.memory-alpha.org/wiki/Boolean_gun
The phaser rifle A type-3 phaser (often simply referred to as a phaser rifle) was the Federation classification of the rifle variation of the standard Starfleet phaser weapon.
http://en.memory-alpha.org/wiki/Type_3_phaser
5. Athleticism
6. Battle Savvy/Awareness
I wanted to post the videos afterwards and describe the details as some encompass multiple advantages in the same video.
1.) Khan introducing himself
1. 25-30 seconds --Genetically engineered to be superior.
2. 1:25--1:29--"Because I am better." Kirk says, at what? Khan replies, "Everything."
3. 1:35-1:39--"Admiral Marcus needed a warrior's mind, my mind."
4. 1:47-1:52--"He wanted to explore my savagery. Intellect alone is useless in a fight."
http://m.youtube.com/watch?v=4LThIRkpYtI
2.) Khan crushing Marcus' skull.
33 seconds into the video. Super strength feat far beyond anything we have seen from Darth Vader.
http://m.youtube.com/watch?v=d-gkvrkvH_Q
3.) Khan attacks Starfleet.
35-47: Khan knew Starfleet protocol and to use the bombing to set the Starfleet officers up to attack at this precise moment of vulnerability and confusion.
http://m.youtube.com/watch?v=g1mTJS0L_Hs
4.) Khan takes on Klingons and subjugates Spock, Uhura, and Kirk.
55 seconds: Khan begins his assault on the Klingons.
1:17: Khan's plasma mini cannon shows its impressive firepower capable of taking out the Klingon ship with one blast.
1:26--1:37: Kirk takes on a Klingon in hand to hand combat while we see Spock taking one out with an accurate blast from his phaser weapon.
1:39--1:41: Khan use the Boolean gun to physically take out an incoming threat and having the superhuman awareness to then switch to long ranged threats with his other weapon.
1:47--1:48: We see Khan taking two Klingons out simultaneously.
1:51: Here we see Kirk shoot down a Klingon.
2:02--2:06: The Klingon reinforcements arrive onto the scene.
2:12--2:15: Kirk's strength give him the breakaway he needs to take out the Klingon before being overwhelmed by the next two.
2:18--2:21: The damage the Boolean gun does to a humanoid body with body armor.
2:25--2:27: Spock, Uhura, and Kirk regroup after Khan destroys the Klingons seek refuge. They are in awe of Khan's fighting skill and abilities.
2:28--2:29: Khan's Boolean gun destroying another ship.
2:40--2:48: Khan eradicating more Klingons.
2:51--2:54: Khan's amazing athleticism. Look at the superhuman distance he jumps with heavy clothing on as well using amazing accuracy while wielding his plasma rifle weapon.
2:45--2:46: Khan shows off his quickly his plasma rifle can fire off successive blasts. These are much quicker than the laser blasts Jango rattled off in a longer time span against Obi Wan.
^^Very Important
2:55--3:01: Khan's incredible skill and hand to hand combat by decimating the Klingons in close quarters combat.
3:07--3:08: Khan easily shoots Spock's gun away before he can react.
http://m.youtube.com/watch?v=K0cFLb-JmaQ
5.) Khan's melee combat and tactical awareness aboard Vengeance.
51-53:
"They know they won't be able to use their weapons here without destabilizing warpcore this giving us the advantage." Khan assesses the current situation he is in and puts himself in an advantageous position. It doesn't take a genius to know that you have an advantage in this scenario although he is brilliant. Khan will know immediately to mow down his opponent whose primary weapon is a laser sword.
1:57-2:07: We see how formidable Khan is in close quarters combat via his superhuman hand to hand combat skill.
2:08: Look at the distance the kick drives the man backwards. The kick also seems to put the man down. Comparing Khan's kicks to Obi and Anakin's is downright laughable.
http://m.youtube.com/watch?v=uT8npGLg2g8
6.) Khan crash lands onto earth.
1:28-1:29 in--There's no way anyone could survive. Spock responds, He could.
2:02-2:05-- Khan jumps thirty meters. That equals around 98.4 feet. This is a superhuman display of athleticism.
3:55-3:59-- The necrotic host is brought back to life due to Khan's blood previously being injected into it. This means his blood is incredibly effective at healing to the point that in the right conditions Khan's blood can resurrect a life.
http://m.youtube.com/watch?v=zMwTbrA7v1I
7.) Khan vs. Spock fight.
1. 29-31 seconds : Bear witness to Khan hurtling himself aboard the ship.
36-37 seconds: Spock also displays superhuman athleticism jumping to grab ahold of the moving platform ship.
1:07 to 1:13 seconds in Khan resists the nerve pinch that ko'd Kirk in a few seconds.
Spock nerve pinches Kirk.
44 seconds to 46 seconds is how long it takes for Spock to knock Kirk out.
http://m.youtube.com/watch?v=HKs4bZHGcOk
1:32-1:33: Khan punches Spock backwards multiple feet in rather impressive fashion.
2:53--3:05: Khan is in the process of defeating Spock via crushing his skull.
3:08-3:20: Uhura stun blasts him 8 times showing off his impressive resiliency/healing factor after the crash landing on Earth and engaging Spock for a knock down drag out fight after these two both sprinted a considerable distance.
http://m.youtube.com/watch?v=rWUDKY7E8ok
All of this evidence points to one inevitable outcome. Khan Noonien Singh is superhumanly accurate with his weaponry, incredibly ruthless, and has the necessary firepower to cut down Darth Vader before he closes the distance between the two combatants. There is no evidence of Darth Vader blocking anything this powerful or as wide as the bursts of energy from the Boolean gun. On top of that crucial point the phaser rifle can fire far faster successive blasts than what the Jedi are used to defending against in the Star Wars universe..
Darth Vader is prone to critical errors during combat due his own self inflated ego aka arrogance in his abilities.. Do not forget the starting distance between the two combatants is the distance between Uhura and Khan at the start of the Khan/Klingon on their homeworld called Kronos. Khan Noonien Singh's superhuman battle savvy coupled with his ruthlessness will definitely get the better of the arrogant Darth Vader.