"Can't"? "Hopeless"? First you are way overstating the case here.
Just comparing classes straight up the fear save is only 4 points behind any other class at 10th level through 13th level. "Can't" is not remotely accurate.
One feat, which the fighter has plenty of, and you erase half the difference right there. And if you design a grizzled NCO (defined in this case by ability to resist fear) with an 8 WIS, then you are not making an effort to design what you claim. So the disadvantage is quite minor and quite acceptable. The claim of "can't" is either poorly considered or disingenuous.
(As an aside, the fighter in Pathfinder gets a bonus specifically to fear saves that keeps them at or just -1 behind a good will save at every level)
When you talk about skills you are apparently presuming a generic build fighter and then declaring him poor at given specialties. You can easily build these options. Certainly I've always found it common that gaining a class skill is easy. But even without that an appropriate character build for the concept and simply taking skill focus goes a long way. Depending on how you build it, there may be no difference, or the pure fighter may lag slightly. But, again, "incompetence" is either an incredibly poor choice of words, or is not an honest presentation.
But then we get to the real issue, because all this above is just playing with a deck stacked in your favor.
Well, let us consider a 15th level Fighter, then. Elite Array is the design statistics for 3rd edition (let's ignore Pathfinder for a moment and look @ 3.5E).
So S 15 (+3 leveling) D 13 Cn 14 I 10 W 12 C 8
would be a normal array. Presume you have spent a feat on Iron Will (you have a lot of feats) and have a +3 save item. I would expect a will save of +5 (base) + 3 item +2 feat and +1 stat. That is +11.
What are some level appropriate challenges to will? A Horned Devil is about the right CR has a DC 23 fear aura (need a 12 to save), just walking into the aura. And that is with a strong focus on saving throws, taking the extra feat and focusing on wisdom instead of intelligence or charisma. Without the feat and with a wisdom of 10, the odds are much worse (needs a 15 to pass) and that isn't a ridiculous fighter build. A level appropriate Red Dragon is worse (DC 24) although I amdit the consequences are minor.
The wizard, on the other hand, also gets bonus feats (from a different slect list) and has a +9 base save at this level (which is picked to make the save difference minimal; it's worse one level up or down) so, with a 10 wisdom is better than the fighter at standing his ground despite lacking a feat and having a weaker wisdom score (presuming that the wizard also invests in save boosting items).
But the killer is a dominate person spell from a level appropriate NPC wizard (DC is 10 + 5 + between 5 and 7 for INT) = 20 to 22 (roughly even odds).
Or what about social skills? Sense Motive is DC 25 to detect a charmed person. Even with 2 ranks in the skill (even if humn, we are talking only 48 skill points total), the fighter can't ever make this check. For a DC 15 domination effect, he has a +3 (and that is with actually investing in it).
Or what about spot and listen? A CR 11 Dread wraith has a Hide of +24 (versus a spot of +1, maybe plus +3 with a couple of ranks).
A 15th level rogue with 8 wis would likely have spot +17, listen +17 and would be quite competent to spot the Dread Wraith (impossible for the Fighter).
It is true that saves are not as bad as the skills (and I apologize for any hyperbole). But the skills are pretty bad. Some of this is niche protection (the rogue is really needed to detect problems upfront). But it also means that the fighter lags way behind the rest.
Consider, spot and listen. A rogue with normal wisdom will still likely have a +18 to spot a hidden foe. A Fighter who wants combat expertise is unlikely to have more than a 10 in wisdom and might well have a +0 spot modifier. Rolls of 1 or 2 by the rogue are as effective as rolls of 19 or 20 by the fighter. That slowly makes things that challenge the rogue, impossible for the fighter.
Even worse happens if the skill aligns with a attribute that the class pushes. Imagine a Druid investing in spot (likely with a 22 wisdom by level 15) or a bard investing in diplomacy. Since a "1" is not an automatic failure, these classes can do better than a fighter with a modest investment in the skill (say 5 ranks) without even rolling. And 5 cross class skill ranks is 10 skill points from a class with a base of 2 and few advantages to intelligence (and which benefits from being a dwarf, for example).
It's not that this is necessarily unrealitic nor that the class is unplayble but that it does seem to fit fictional archetypes poorly. There are some exceptions (the Iliad seems to be one, Roman gladiators would be another).
This, by the way, is not a comment on the power level of the class. It's capable of being really brutally strong, especially if the full array of 3.5E feats are permitted.
But it is an odd design space for the class, especially since other classes in 3.5E don't have the same issues (Rangers and Monks, for example).
But your mileage may vary.