I've posted something like this before, and I was going to include this in another post I'm writing, but it got a bit long by itself so I'm tossing it up here.
The game is riddled with some pretty crappy choices right out of the gate, but those choices get enshrined by tradition and addressing them becomes a problem. You said ‘One is the Tome of Battle, which made the dying fighter class obsolete once and for all.’, but that’s not really a fair assessment. The Fighter was made obsolete by the Player’s Handbook the moment they gave the Druid a (Core, even) choice of Animal Companions, spellcasting, and Wild Shape that by level 7 could do everything the Fighter could do and then some. More HP, more outgoing damage, more versatility.
Again, this is the PHB only, and I’m not talking about corner-case extreme builds, I’m talking about a Druid who picks up Natural Spell and can access his entire Druid spell list (of up to 4th level) while in the shape of a Giant Crocodile (basic Monster Manual anmal) which has a +11 attack bonus (that’s the bonus of a 7th level Fighter with a +3 Strength bonus and a +1 Enhancement bonus on his weapon), doing 2d8+12 _AND_ a +21 grapple check with Improved Grab (good luck, core fighter). And while the Fighter in our equation has more HP, the Druid can cast a 3d8+7 Cure Serious on himself, which surely makes that irrelevant. This is all entirely aside from his animal companion or anything he decides to summon to help out. I realize that classes shouldn’t be compared to one another, but you can compare them to pretty much anything else and the Fighter offers virtually nothing.
Two levels later the Cleric is joining the Druid just by virtue of being able to cast Righteous Might. Fighter attack bonus (including Iterative), reach, +4 str, +2 con, bonuses to your AC, damage reduction, etc. 1 round of spellcasting and you’re at least on par with the fighter in terms of HP, Attack Bonus, and maybe Damage depending on a fighter’s focus. And you can STILL toss out a Flame Strike if need be, doing more damage in a single round if there are numerous enemies than the Fighter will probably do the whole combat at this level. Or, again, curative spells negating any real HP difference. Again, this is all PHB only.
Meanwhile the fighter has to choose what he’s focusing on, since his only real class feature is bonus feats. Except entire trees of his feats are negated by spells and abilities that start to become more and more common, which leaves focusing on damage, and at the end of the day that’s seriously single-target focused. Which in reality usually means standing up front waiting for the enemy to fail its save against one of the many, many, many spells that failing a save against will kill or incapacitate it. Assuming the Druid isn’t already up there tanking with his bear companion and summoned lions.
Even the Rogue is often doing a better job than the Fighter at its basic focus: Doing damage. By 7th level the Rogue has their weapon +4d6 damage on sneak attacks, and those aren’t exactly difficult to get. That’s on top of being a skill monkey of the highest order (lolfighterskills), and probably having higher AC unless the Fighter is in plate mail (with all the drawbacks that come with it).
About the only classes that drift behind the Fighter in Core are the Monk and the Bard, and even the Bard has the skillmonkey and spellcasting thing going for them. The Fighter has been dead since Core, it just keeps getting played because there’s no other class that fits the theme of ‘sword wielding tactical warrior’ (I didn’t go into Barbarian, because it’s a much more iffy thing, and really pretty close between them). Until Tome of Battle brought out the Warblade. A Fighter who actually gets bonuses for having some Intelligence? Who isn’t totally reliant on the Wizard when fighting something with damage reduction? Who can actually pull off the sort of feats of martial prowess that the ‘Fighter’ in so many of the books we read and movies we watch is able to, when the actual Fighter-class would be reaching for a spellcaster or magic items or something else entirely sissy-like? Awesome.
Player’s Handbook was the death kneel for the Fighter-as-a-class, Tome of Battle was the resurrection of the Fighter-as-a-character. And since I’m more interested in being able to describe my character than I am dedicated to a specific class, that’s a good thing, to my mind.
Note: I'm addressing another poster a few times here, hence the odd syntax here and there.