Hasn't come up here yet, so I say it: Nobody forces you to do sneak attacks. Just like noone forces a fighter to use heavy armor and a tower shield. We don't stereotype fighters as users of longsword/fullplate/tower shield, so we shouldn't stereotype rogues as sneak attackers. If they don't want to use it, they just don't. It's still a great class, what with all those skill points and the defensive capability.
Someone mentioned the "we're not the thieves anymore". Actually, sneak attack (or backstab) isn't something I imagine when I think of a thief. It's something for an assassin. The 3e rogue is not stereotyped anymore mainly because the name. With "thief" people assumed that he'd have loose fingers and would steal from everyone just for kicks - including other party members, powerful guys and dragons. "Rogue" might not be that trustworthy, but it's better than "thief". But I digress..
Making it a skill would be bad. It would not only break the whole skill system, it also is more fitting as feat. So we could make it a feat and give rogues bonus feats at every odd level. Bonus feat list: Skill Focus, Sneak Attack, all +2/2Skill feats that involve any of the rogue class skills, Weapon Finesse (and yes, I think that BAB +1 should be taken from the requirements), maybe the Dodge and/or Combat Expertise chains.
Feat:
Sneak Attack [General, Rogue]
You can hit foes where it hurts, doing +1d6 damage
Prerequisites: See text
Benefit: Insert the write-up about Sneak attack here
Special: For taking it for the first time, you must have either rogue Level 1 or character level 4. You can take it more than more than once, and its effects stack. For every instance, the prerequisite rogue level increases by 1 and the character level by 4.
So A rogue can take it at 1st,3rd,5th and so on, or he could skip some (or all) uses for other feats.
Rokugan, besides having another Core Class with Sneak Attack (the ninja, which gets full BAB and full sneak attack - but a variant fighter from UA could get that, too, and d10 to boot) it has Feats (for Scorpions - the clan, not the vermin, though some call the Scorpion vermin...) to grant an individual +1d6 sneak attack. It can be taken several times, I think 3 or 5.