Well...One is vital for an extreme character build. The other is has abit more use for the exact opposite character build. Both are not that great really.

Personalty I dislike both "Fast Shot" and "Trigger Discipline". "Good Natured" as already stated and "Small Frame" for the +1 SPECIAL works very nicely. Don't let the penalty of Small Frame scare you off as it's one that can be controlled by just not taking damage.

I am curious whether Trigger Discipline" or "Fast Hands" is "vital"?

I do agree Good Natured + Small Frame is "rule of thumb" for range character. However sniper seems to have excess in both skill and stats point.

Since I wanted an effective and ammunition-saving sniping style for my char I chose "trigger discipline" as a trait, leveled up to 8 and then read this;

http://fallout.wikia.com/wiki/Trigger_Discipline

Right now I'm disappointed with Bethesda (and my own choice) since it might have been wiser for me to chose Fast Shot for my sniper, which does sound a bit opposite-George-like, and Trigger Discipline for a run'n gun type, which isn't my thing really. It's a bit ironical, since I during charachter creation thought about my Oblvion-leveling-experiences and went "hmmm....I hope I'm not going to regret this...I'm sure I'll regret at least one of my traits" :cryvaultboy:

As for now my charachter is a bit slow in VATS mode, but I've managed ok, although I have no mathematical formula to give you for the pros and cons. But I'm not going to choose that trait again for a sniper, that's pretty certain, although it might be fine for a shotgun-style-charachter.

The Good Natured-trait is very good though, at least if you're focusing on one weapon category, I'm glaaaaad I took that one.

I'm about to start my first pure sniper as well, so am reading this with interest.

I would have said that Built to Destroy is an absolute essential trait for a sniper. It increases your critical hit chance, which is pretty much what a sniper is all about. If you don't kill something in one shot, then you aren't a very good sniper. Therefore 1st Recon beret, Built to Destroy and high Luck seem pretty much mandatory to me.

Another question I have been thinking about is a good sidearm for close quarters combat. There are plenty of buildings and vaults to explore, so I would imagine this is not the sniper's natural home. So a hard hitting close quarters weapon is also required. I think That Gun is a good choice, since it has a 2.5x critical multiplier, which mixes perfectly with the above traits. It also looks cool.

pretty big spoiler ahead

With Built to Destroy, your weapons will degrade faster. This may be a problem if you plan to use a slenced Sniper Rifle as your main sniping tool. Sniper Rifles degrade annoyingly quickly and have limited repair options even with the Jury Rigging perk. They are classified as "two-handed automatic guns"; almost all weapons in that category are expensive and rare, with the exception of Service Rifles which aren't expensive but are still uncommon. (Well, unless you plan to murder many NCR troopers). You may have to carry a few Weapons Repair Kits with you every time you go into the field, and get Raul as your companion as soon as possible. You also might want to carry a more durable spare for shooting single targets- a scoped Hunting Rifle or a Trail Carbine.

On the other hand, if you plan to go Cowboy and use a scoped Trail Carbine as your primary sniping tool, then Built to Destroy is awesome. Cowboy weapons, in addition to being awesomely powerful, are EXTREMELY durable AND dirt cheap to repair. A Trail Carbine can be repaired with BB guns, Varmint rifles, Cowboy Repeaters and Caravan Shotguns- all these are cheap and easily found. Occasional hunting trips into Fiend territory should keep you well-stocked.

As for "sidearm"- That Gun is easily the most disappointing weapon in the game. The high critical change doesn't make much difference when the crit damage svcks.

Here's the setups I would recommend:

"Power" sniper:
Anti-Materiel Rifle
Riot Shotgun or Dinner Bell

"Stealth freak" sniper:
Silenced Sniper Rifle
Silenced 12.7mm SMG OR 12.7mm Pistol (the SMG is vastly more powerful, but repair issues are the same as for the Sniper Rifle. Also, 12.7 ammo is relatively rare and pricy, althought it's worth the price).

"Commando"/ military sniper:
Silenced Sniper Rifle
Light Machinegun (repair issues again, but ammunition is common)

"Hunter" (themed build if you feel like it):
Scoped Hunting Rifle
Dinner Bell or fully modded Hunting Shotgun

Cowboy:
Scoped Trail Carbine
Brush Gun or Ranger Sequoia

Not the best by any measure. It is even inferior to the standard version of the same weapon, as the most important mod is not available.

Except with the "power" sniper you would likely fall back to you shotgun after a while because AMR is so heavy and useless in unfocused vision range.

I also recommend Silenced 10mm over 12.7mm; SMG's clip is too small and Pistol's spread is too large.

As for Commando, I would say Marksmen Carbine would get the job done. Or Sniper Rifle with an SMG (either 9mm or 10mm).