Your question revolves around the mechanical quality of various options, and I will therefore give an optimizer’s perspective to the issues. I will use words like “should” or even “must” without qualification, so I am stating up front that this entire answer is qualified as applying if you want to optimize your character.
Unfortunately, your question of regular fighter vs. sneak attack thug is problematic. Because of the realities of 3.5, which favors heavy multiclassing for martial characters, this is a false dichotomy. Thus, I’m going to introduce my answer with a significant tangent into metagame theory surrounding the fighter class. I consider this critical background information to discussing the sneak attack thug.
Why take fighter levels: Feats and BAB
The fighter is a weak class; feats are all he gets. Feats are valuable, but class features are (or should be) more so. The fighter is also a full-BAB class, which may matter to you but may not. Generally, these features are most critical when it comes to qualifying for prestige classes.
In core, there simply aren’t enough feats that are good enough to justify getting only feats as your class features. Outside of core, there are more than enough feats, but the alternatives to fighter get that much better. In other words, (the regular) fighter is a class you only take if you are desperate for feats and cannot lose any BAB (if you can lose BAB, cleric, monk, and psychic warrior are often more effective ways to get feats).
The only time you should be “desperate” for feats is when you want to use a prestige class that requires a lot of them.
Base attack bonus
As for BAB, it’s important but not the be-all, end-all, unless you’re aiming to enter a prestige class that has BAB as its primary “gatekeeper” (that is, you can enter the class as soon as you have enough BAB, so missing out on BAB directly delays entry into the prestige class). If you want to enter a class that requires BAB +3, but 8 ranks in a skill, missing some BAB won’t matter much because you wouldn’t be able to enter until you got the 8 ranks anyway. On the flip side, if a class requires BAB +5 but 4 ranks, missing a BAB puts you a level behind, which is a fairly big deal.
So ultimately, fighter is a class that is best used to ease entry into prestige classes. In low-level games, where feats are more scarce, two levels (for a feat per level) can be good, too. But usually, you get enough feats to get the ones you actually want without needing fighter levels, which means those levels are better spent elsewhere.
Reality: fighters multiclass
Because fighter levels are primarily useful for entering prestige classes, it almost goes without saying that fighters should not literally be Fighter 20. In reality, they shouldn’t actually be more than Fighter 2 most of the time; a feat-per-level is solid; a feat-every-other-level is not. But most prestige classes cannot be entered at level 3. Thus, you need other classes.
Most groups do not use multiclass penalties; they are ineffective at doing what they were intended for (limit multiclassing) and many groups feel that was an undesirable goal in the first place (multiclassing is one of the biggest strengths of the d20 system).
That said, as a Fighter 2, you don’t have to worry about it. You do not suffer multiclass penalties as long as all your classes are within one level of each other, which means you can be Fighter 2, Fighter 2/X 1, Fighter 2/X 2, and Fighter 2/X 3 (or Fighter 2/X 1/Y 2 or whatever) without any multiclass penalties. Prestige classes also do not count, so if you enter a prestige class at 6th, you’ll never see a penalty.
Typical options: barbarian, cleric, ranger, warblade
Barbarian and cleric are two of the best single-level dips in the game. Barbarian 1 gives Rage, and with Complete Champion, Pounce. Cleric gives a smattering of spells, two domains (which may mean two bonus feats, or things you can’t get as feats), and Turn Undead which can be used with Divine feats. Complete Champion again improves that option, adding the excellent Devotion feats as alternatives for Domains, including the fantastic Travel Devotion. Because of Pounce and Travel Devotion, basically every melee character ever should have at least one level of either barbarian or cleric if Complete Champion is in play.
If fighter is your choice for entering prestige classes that require a lot of feats as well as BAB, ranger is your choice for entering prestige classes that require a lot of skill ranks as well as BAB. Full BAB and 6+Int skills is solid. The actual ranger class features are fairly meh, but if you need any of those feats, hey, more free feats.
Warblade from Tome of Battle is an excellent class, and it multiclasses very nicely (half your non-warblade levels count towards your warblade level for the sake of the warblade’s maneuvers). It’s often seen as “what the fighter should have been,” but if you need a bunch of feats, taking fighter levels before entering warblade works quite nicely.
Sneak Attack Thug and Rogue
What I’ve established, hopefully, is that you should not compare a Sneak Attack Thug 20 to a Fighter 20; neither option is likely or desirable. Rather, you’re talking about a Fighter 2/something 3/prestige class 10/another thing 5 or something, and wondering how the sneak attack thug fits into this picture.
Some basic facts about the sneak attack thug
The Sneak Attack fighter is better in combat than a (core) rogue. He arguably gets 1d6 more Sneak Attack (thanks to the bonus feats on both 1st and 2nd level), he has full BAB so iterative attacks come online sooner. The thug is more skilled than a regular fighter by a fair margin, though far, far less so than the rogue.
But ultimately, the Sneak Attack thug’s only schtick is combat, and there are better ways to do combat than Sneak Attack. Simple example is a mounted fighter/barbarian charger with a lance and Power Attack. Another good one is the so-called horizon tripper, taking advantage of Improved Trip’s excellent lock-down by using Combat Reflexes, and comboing fighter, barbarian, and ranger in order to enter horizon walker for excellent mobility.
Considerations of the rogue
Meanwhile, the rogue is generally seen as a higher “tier” class than the fighter. In combat, the class is lackluster; Sneak Attack is non-trivial to set up, relies on feat-intensive dual-wielding for optimal damage, and even with all that it doesn’t keep up, damage-wise, with a good charger.
But the rogue is still better. All a charger can do is damage; a rogue can do so much more. The thug adds in a fair few more skills, but the class skill list is still paltry compared to the rogue’s, and the rogue probably has more than twice as many skill points. Most importantly, the rogue gets Use Magic Device in-class, and that skill is amazing.
If you do not need feats very badly, you don’t really want (regular) fighter levels. The sneak attack fighter replaces these with Sneak Attack; not a bad trade, but the rogue gets so much more along with Sneak Attack.
So you should only take fighter levels if you really need BAB and feats or Sneak Attack. If you’re a rogue, stick with rogue unless you need BAB for something. If you want some BAB, but aren’t hurting for feats, a sneak attack thug level will get you BAB without costing you Sneak Attack, and it’ll hurt your skills at least somewhat less. If you really need BAB and feats, then regular fighter is your best bet.