First of all the Fighter is illustrated as having these problems but note that these are also problems for the Barbarian, Paladin, Ranger and Bard. It seems pretty universal.
Generally, when the debate is about "fighter vs. wizard" it means "primary martial types vs. full casters," so "
fighters can't have nice things," "
fighters have issues without lots of magic items," etc. includes other full BAB classes.
The Fighter is getting a lot of heat in the area of full attack dependence but lets face it that is a design feature of the game. To change that is to change the game.
Not all that much. In 1e and 2e, you could make all your attacks and still move, and only fighters (and in this case I
do mean just the fighter and its subclasses) could make multiple attacks. Changing the game to require full attacks in 3e was a step backwards.
Countering debuffs is a joke too, what do you expect these classes to have? I agree with the common house rule that Stringburka puts forth with the altered save progression (it is in my house rules). I see this one as a no brainer because at upper levels DC for spells outstrips save bonuses by quite a large margin for single classed characters. At +1/2 level you simplify multiclassing too. But really what do you want them to do to debuff? Give them evasion, mettle or once-per-battle Concentration checks that cancel the first Will save thrown against them? No, that is not their flavor. If you want to get evasion multiclass it is easy enough.
Not their flavor? It used to be (again, 1e and 2e) that by the time you got past, say, 13th level, fighters made pretty much every save on a 2+. Fighters were just as much the "Puny wizard, your spells cannot stop me!" type as the "I'm going to bash your head in with a blunt object!" type. Mettle, evasion, save bonuses, and other ways to avoid/ignore debuffs are right up their alley.
The only argument that I have seen worth its salt, that is leveled directly at the fighter is that it is a 2 or 4 level class. This is not to say that a level 15 fighter cannot be effective but more that the fighter is suboptimal when built that way. This is two problems that the fighter has: it is very easy and effective for Full BAB characters to multi-class, and fighter abilities do not scale or get better so there is no reason to keep leveling with them.
I tackle both problems in my House rules.
First, in a round about way I keep the fighters effectiveness even after you multi-class (bonus fighter feats) by allowing you to add bonus levels similar to how "initiator levels" stack (+1/2 level). I require a feat to be spent to get that bonus but at that point fighters class features (bonus feats) stick around and become better even while advancing in another class.
Second, I remove the weapon specialization feat chain and instead make them a class feature for the fighter that scales. Any weapon you have weapon focus with also gives a damage bonus equal to 1 + 1/4 your fighter level. This gives a reason to continue to gain fighter levels and it lowers their feat tax and improves their combat effectiveness all in one fell swoop.
Both are good ideas; more feats are always helpful, and taking the normal Focus/Spec chain is usually worthless.
I have played Bo9S extensively in several campaigns and have designed several other characters out of that book. I feel it is the most broken book ever published for 3.5, it even beats out the expanded psionics handbook. I know you and many others do not feel this way but from my experience with it I do. I felt like I was cheating... Conceptually it has some neat ideas, however its implementation is way out of whack.
Having seen your arguments and houserules, I don't see how this is the case. Maneuvers could just as easily be feats, you let fighters gain feats via a version of IL, and so forth...yet warblades are horribly broken? Steel Wind is Cleave, but you don't have to drop an enemy for the second attack. Wolf Fang Strike is TWF, but you don't take the -2 penalty on each. The entire Setting Sun discipline is "I can do combat maneuvers against bigger foes without sucking." All of these "broken" maneuvers are basically taking the sub-par feats and making them usable.
If you consider core melee to be mostly fine and ToB and XPH (some of the most balanced books in 3e) to be broken, I don't know if any conversation about the fighter's (= core melee's) problems can have a common balance point.