Different attacks on same species of Pokémon in Pokémon Go

I'm not sure there's an answer to why, beyond "that's what the dice / random number generator chose", buy you can likely power them up to the same max CP (they just started at different initial values). I suspect it can make more sense to power up a Pokémon who starts out with a lower CP but better attacks, rather than spending stardust and candies powering up an already-higher CP instance of the same Pokémon who has lesser attacks.

Moves are completely random. In your example, your two Scyther's have their particular move sets because those are the moves that "rolled" when the game determined¹ it was time to roll that Pokémon's move set.

Using your example, you can be lucky, and run into a high-CP Scyther with two strong moves. You can also be unlucky, and run into a low-CP Scyther with two weak moves.

There are other things you should take into consideration, when looking at the moves of a Pokémon to determine its value:

• Moves have types, too: Each move has a particular type. While we are yet to determine if there is any bonus for using a move that has the same type as the Pokémon that uses it, the move type will play a part in determining the overall damage, when you use it against opponent Pokémon. You might consider aiming for two separate types, to offer increases strategical ability when faced with a Pokémon that is resistant to one of your types. You might consider sticking to the same type, in effort to create a "pure".
• Moves change during evolution: If you intend to evolve your Pokémon, it is worth addressing the fact that your moves will "re-shuffle", when the Pokémon evolves. You may gain more powerful moves, but you may also gain weaker moves. Regardless, you should not consider your move set at all, if you intend to evolve.
• Moves are set: At the current time, there is no way to alter the moves of your Pokémon, other than evolution. If you have a Pokémon with a move set you favor more than a duplicate Pokémon with higher CP, you should favor the Pokémon with the desired move set. You can always upgrade the Pokémon's CP to match the duplicate's.
• Eevee's moves DO NOT appear to reflect the evolution: As pointed out by another user, there is a rumor being spread by Reddit that the particular moves rolled on an Eevee will determine the variation that Eevee will evolve in to. I am addressing this only because we now know this to be false. Unfortunately, the Eeveelutions are apparently random, and we at least know that it is not determined by the move set.

_{¹ For the point of accuracy, the move set may be determined when you first encounter the Pokémon, or may not be determined until you actually capture the Pokémon, and the move set is first actually presented to the player. At the current time, we do not have enough information to know when this occurs.}