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.
Bonus feats
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.
Conclusion
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.
Multiclass Penalties
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.
Conclusion
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.
The History
This actually goes all the way back to the first OD&D supplement, Greyhawk. The maximum spell level a Magic-User could cast was now limited by his Intelligence. Although interestingly, Clerics were explicitly not limited by Wisdom. The justification was that, unlike Magic-Users, a Cleric's spells were divine gifts, not based upon their skill. Intelligence also limited how many spells the Magic-User had.
Speculating, this was probably partly simulationist and partly for mechanical reasons. Arcane magical ability is tied intelligence, both lore-wise and in the the Magic-User's prime requisite was Intelligence. High level spells are more complex (the spell level system is a direct mapping from Chainmail's complexity system) so there's logic to a smart Magic-User being able to handle more complex spells than an average one.
Your Ability Scores had little mechanical impact in OD&D, primarily a bonus to experience gain. Greyhawk began increasing the existing, minor bonuses and penalties and adding new ones. Intelligence affecting Magic-Users spells was part of this increasing affects from Ability Scores. And only Magic-Users with an Intelligence below 11 were actually losing anything compared to the core game, because the 7-9 level spells were added with Greyhawk, and did not exist before ability limits.
This Ability Score limit spread to Clerics with AD&D. High level spells required a certain Wisdom and a low Wisdom could cause spell failure.
You may have noticed that Ability Scores were only limiting the casting of high level spells. As KRyan touched on, this is because of Prime Requisites / Ability Score requirements. RAW, you couldn't even play a caster with a below average Ability Score in their Prime Requisite.
The Implications
So there's the historical precedent, which explains where it comes from. Was there any other reason to carry it forward, beyond tradition? It makes your Ability Score have a greater effect on your casting. The fact that spell strength is often not based on your Ability Score seems like it could be unbalancing to ignore the Ability Score requirement. I doubt it would be that bad, but I'd ask a optimization expert about it.
I personally don't have a problem with the idea that magic is too complicated for the average (Ability Score 10) person to grasp, and the smarter/wiser you are the more complicated spells you can comprehend and harness. It seems intuitive me, but if it doesn't to you and your players, I say house-rule away.
Best Answer
4th-level and higher spells are beyond the reach of mortal spellcasters
Stuff like angels, demons, and dragons might be able to manage such feats of magical prowess, but your humans, dwarves, and elves cannot. Eliminating 4th-level and higher spells from the game is actually the point of E6 – while all spell levels tend to have fantastically efficient options, 4th-level spells is where it starts to get into the “there is no answer to this without magic” region.
For example, grease or glitterdust may be much more potent singular actions than anything a warrior can do, but a warrior can avoid the grease, make the glitterdust save, have ranks in Balance or the Blind-fight feat, and so on. There are answers. If you drop solid fog on a mundane warrior, he’s just out of the fight for several rounds, and there’s basically nothing he can do about it.
Certain, select 4th-level or higher spells may become available to the players at the DM’s discretion, but these are always going to be plot devices – artifact-grade items provide them, or lengthy and complicated rituals are necessary (quite possibly requiring side-quests to gather the necessary materials). But the players never get 4th-level or higher spell slots to do with as they please. There are a few tricks that, by strict-RAW, would allow them: it is strongly recommended that these get banned from the beginning of the game.