The fighter suffers from a problem that every mundane in Dungeons and Dragons faces to varying extremes, but the fighter
exemplifies it; he is tied at his core to
fighting and nothing but that. Outside of combat, even with a clever player, there is little he can do. He has few skills, fewer skill points, no class features and a genuinely weak identity. What does the image of a "wizard" conjure up? Think on that mental picture then on that of a "fighter". The fighter's variations and iterations are much more limited creatively there at least.
The fighter in Third Edition namely, came early on as a core class and the developers overvalued the powers of combat based feats and most feats in general. "Power creep" is normal, but the fighter has
nothing beyond much of 6th level that a spellcaster cannot generally do better. Clerics? Take the War domain and just about anything else you desire, invest your feats as though you were a fighter and you will still come out on top. Why? Magic is powerful and nothing in a fighter's repotoire can compete with it.
One spell more or less does what an entire class does; that is not counting other game changers even a battle centric cleric (or similarly designated spellcaster) can casually toss about.
Fighters face an interesting issue in that they have little to no power
without supplement books. A wizard, druid, cleric or sorcerer? While more books is always better, their power level does not usually increase that much; the druid is a famous example of that, having almost no prestige classes worthwhile and those that are, are totally broken or break even trades. Wizards are pretty much restricted to Shadowcraft Mage, Incantatrix, Initiate of the Seven Fold Veil and other similar full casting classes, which they are losing nothing for by taking it.
Fighters? I honestly cannot name
one fighter prestige class that is iconic in terms of pure potency and as a direct upgrade to fighter. Most are pure flavor or
marginal in improvement like the Kensei, Exotic Weapon Master, or have easy to access spellcasting like Suel Arcanamach or Pious Templar.
Another way to think of this is, why be a fighter when a barbarian does it better? Sure, more feats, but the barbarian has actual class features and his prestige classes are usually top notch for melee, like Bear Warrior, Frenzied Berserker, Runescarred Berserker, Champion of Gwynharwyf, Primeval, Weretouche Master and the like. His base rage alone, without variants, is better than about three feats
combined. Using variants? A kitted out otherwise 20th level barbarian is
miles ahead of his 20th fighter competitor just by getting the Pounce special ability alone. Whirling Frenzy, Pounce, Wolf Totem, or Devil's Luck just to name a few.
Going another route, the fighter isn't dynamic. He spends his entire turn trying to move to his target and hit once, than another turn trying to full-attack, assuming he isn't interrupted. Sure, he
should try to trip or disarm, but most Dungeon Masters get pretty tired of the routine and most monsters by pure design begin to just ignore that at higher levels, size increases or as magic becomes more available. Dedicated casters can, for the most part, pick and choose what they do and how every day. Spells can be really varied, such as the humble but powerful Entangle, hilarity of Glitterdust, crazy of Shapechange, raw power of Sleep, or even the lowly but reliable Spiritual Weapon.
Sadly even a well picked animal companion like a default big cat for a druid is going to out fight a fighter... and at worst, if killed, the druid gets a new one by the next day with no actual penalty. Not fond of cats? Dinosaurs, bears and wolves have a pretty solid place. In fact, you can even choose their feats for them so you can build their identity around whatever you want them to do.
The fighter isn't a class worth taking by itself. In fact, using it as a dip is debatable. The
only incarnation of fighter that lives up to any real standard is the Fifth Edition fighter because it has so many solid and consistently useful abilities. Action Surge and four attacks alone make it formidable, ignoring all else. It validates it's existence by being good at what it says on the tin and everything thereafter just serving to support it.
In conclusion, there is nothing unique a fighter can bring to the table that another class cannot do better overall. Want a better fighter? Play a War cleric, psychic warrior, warblade, barbarian, duskblade or the sort. The sad truth is that you get versatility and options by doing so.