1. Squadsight literally most OP ability in game. Not even close pick.
2. If you are using your pistol on your sniper you are using him wrong. If I had the "arc thrower as pistol" mod I would put an arc thrower on the sniper vs pistol. With PSI abilities, reloading, etc. you should never be using a pistol for your second action. Period. Not even close.
3. Scanners can be useful early game (before stealth gene and/or having your MEC's which scout) but mid-end game are utterly worthless. On the flip side disabling shot is very situational and only situational mid-end game vs some of the most difficult enemies in the game. Strong pick here for disabling shot

4. Your sniper should have all or most of the medals, that with gene and damn good ground mean your sniper literally has 100% chance to hit most of the game. This makes the first ability literally useless. Not even close pick.
5. In the zone is the second most OP ability in the game, making both OP skills on Sniper class. Use your MEC's grenades and/or mines to blow up enemies cover and then once the enemies are coverless you can kill all three in one turn. Same applies for ALL flying units- you will be able to kill all drones first turn 100%.