X and Zero's respective postures when firing their busters says a lot about their experience. X fires with one hand on the buster, steadying his rookie aim. Zero, on the other hand, confidently aims solely with his buster and his other hand by his chest (bosses such as Storm Eagle and Flame Mammoth share this stance). This difference in posture carries on throughout the rest of the series too, with X always using his other hand while Zero fires freely.
Zero telling X that Vile is "designed to be a war machine" is ironic once you know Zero's past. The reason Zero is able to best Vile and X can't, is because Zero himself was designed to be the war machine to end all war machines.
I used to be amused by a discrepancy in Nintendo Power's coverage which issued a "challenge card" claiming that beating Storm Eagle as the first boss was one of the toughest challenges. Half of his moves deal no damage and are simply meant to push X off the ship. Until I realized the real challenge is lacking the foot parts from Chill Penguin's stage. Try beating Storm Eagle without a dash. That can be fairly challenging.
Storm Eagle's bio says he tried to defeat Sigma and lost, forcing him to fight on his side. Storm Eagle is only a challenge without the dash to push against his wind; the other half of Eagle's moves can be dodged or shot down. Against Sigma, he had nothing that could work.
Additionally, Storm Eagle is weak to bladed weapons such as Chameleon Sting or Sonic Slicer (in Xtreme). Sigma's weapon of choice is a beam saber!
One might wonder why, out of all of the weapons in the game, the defensive Rolling Shield is the only weapon (aside from the upgraded X-Buster) that's capable of damaging Sigma's final form. Well, consider the company that Sigma keeps. Sigma knows very well that the majority of his minions are untrustworthy, for one reason or another, save for one: Armored Armadillo, the one most loyal to him and who follows orders without question or ulterior motive. As such, when designing his final form, he made it specifically immune to any form of attack from any Maverick that might turn traitor on him - but saw no need to accommodate for Armadillo's weapon given its defensive nature and that Armadillo would never turn on him.
Wolf Sigma shares its appearance and attacks with Velguarder, such as a flamethrower and a lightning ball attack. Sigma must have really loved his little pet to base his ultimate battle body after it.
Look at Flame Mammoth's stage: a massive furnace made for recycling large amounts of metal... including damaged Reploids, some of which are still active enough to grasp at X as the conveyor belts take them to be melted down. It might seem like just another fire level for us players, but for a Reploid, this is what Fire and Brimstone Hell looks like.
If one ever saw the film Old Yeller, it makes perfect sense as to why Sigma's dog Velguarder's weakness is Shotgun Ice...
