If you get Tunnel Runner, Travel Light and OWB implant, you can crouch-run as fast as normal running.
And do max out Melee and Unarmed, since you need both skills to get Piercing Strike and Slayer. And when you get both Grunt and Cowboy perks, get Chance's Knife, since it got bonus damage from both perks as well as high crit chance... since I figure splinter cells LOVE knives.
I also figure you will be a pistol user... I highly recommend picking up The Professional (Glitched perk, since it actually gives 25% for EVERY critical hits with pistol and not just sneak attacks). Also, you might need most, if not all, the VATS and accuracy related perks, because they will help you to pull off impossible stealth headshots.
As for weapons... It's a shame Li'l Devil isn't silenced because it's like the best pistol in the game for pure hed-sploding crit power (Along with its "easier-going" sister, Lucky) but I guess you can make do with the 12.7mm silenced pistol. But the .45 has a greater fire rate, CAN be silenced, so with max Luck and Finesse, you can safely pepper your target with crits before he can even make his move. Stocked up early on ammunitions, and don't get lazy on changing ammunition for different targets.
Oh and the SPECIAL... Definitely max out Luck and Agility... My recommendation is 5/5/5/1/6/9/9. You maybe concerned with the low Endurance, but I think you have a lot of spare perk points to Intense Training if you plan carefully. And I'm not really sure on how bulletproof splinter cells are, but in the early days of the series, they rely mostly on stealth and weapons mastery instead of magical healing factor and unlimited ammunition.
On equipments... I would recommend Joshua's outfit/Ulysses' duster and 1st recon beret as a combination for potentially ungodly crit with unstoppable VATS prowess... But it's your choice, really, since I know that combo doesn't have a splinter cell feel to it. So if you decide to max crit, do Lonesome Road (or at least Honest Hearts) first for the best effect.
Faction choice... Eh, NCR. Sam has always been a government gimp, even after he became disillusioned and gone rogue (
Spoiler But hey, I guess the government saved his daughter, so the man has the right to be grateful
).
Oh, and if you decides to use melee weapons, remember REMEMBER to get Elijah's Rambling... Keep Elijah's tape to yourself, don't give it to Veronica!