Greetings!
MMADSEN, of course, illustrates the problem with fine precision.

Good work my friend! Snoweel, I'm glad that we have persuaded you to the Dark Side!
Indeed, I believe that much of the emotional resistance comes from many people still either consciously or unconsciously holding on to the mind-set of 1st edition, where a 3rd level character was far more than a 1st level character, and as mmadsen pointed out, a 1st level fighter was quite superior to a "zero-level" npc.
However, with the 3rd edition set of rules, these assumtions need to obviously be reexamined, and thoroughly. In addition, and this is something that I and mmadsen have discussed at some length, and I might add the thought processes are greatly assisted by a bit of Bass Ale and a fine cigar!

We discussed the dynamic that in 1st edition, for example, the skills of a seasoned legionnaire or a frontier-riding witch-hunter priest were largely undefined, and thus, the dm, and the player character, where appropriate, just assumed a vast array of important skills and sub abilities that the player or the dm could call upon to justify any number of bonuses to whatever rolls the dm felt appropriate, or if desired, they might be penciled in to the character sheet or the dm notebook to remind them that the character had spent ten years learning all about expert mountain warfare in Syria, or the witch-hunter priest was an excellent theologian, and a master stonemason and occult investigator.
The problem is that with 3rd edition, many of the skills and special abilities that we just assumed and wrote down as needed in 1st edition are now given a name and precisely and absolutely defined in the rules of 3rd edition. Thus, if your character doesn't have *such and such feats* and *x ranks in these six skills*, well, then that character can't really be all that, now can he? The character either has the feats and skill ranks, or they don't. Furthermore, if the character has only two ranks in such and such skills, well, then they can't really be said to be very knowledgeable about whatever subject, let alone an authority or an expert.
Thus, you get into the problem that I have discussed with mmadsen about a legionnaire having--and needing certain feats, and a range of skills--far more by the way than merely what are assigned as class skills for fighters--and not really having these things until they are 8th level. In 1st edition, you could assume certain things about 2nd or 3rd level fighters, and say they were the legionnaires of the great empire. However, as mmadsen illustrates vividly, 1st level fighters, and their slightly improved 3rd level brethren aren't really up to conquering much more than the local tavern full of drunken thugs--they certainly aren't equipped to be the glorious soldiers conquering a world for a mighty empire, struggling against mighty enemies.
Thus, the inexorable need to reevaluate the assumed levels of various characters that populate the game world.
Now, we have Reapersaurus. How are you? Well, to answer your question, I have no problem at all integrating magic into the world, and having it effect the battlefield in numerous ways. In my campaign, has it made armies obselete? Well, no, it hasn't. Has it made the infantry or knights useless and obselete? No, it hasn't. Mages operate to support and protect the military forces around them, as well as to serve as specialized mass-fire-power shock troops. However, as my friend Dragonblade has learned while playing in my campaign, there is a lot going on. With literally thousands and tens of thousands of troops on the battlefield, with numerous clerics and wizards integrated into both sides forces, all fighting simulataneously, it seems to equal things out, though it makes for a hotter, dramatic sort of fight, with numerous potential turningpoints. The troops still fight, and there are a core group of skills, knowledge, and tactics that remain effective and useful, providing different resources are present and accessible, and variables are accounted for by the high command and effectively, at least on a broad scale, sufficiently adressed. Wizards for example, can and are very effective, and if more than a few of them, or several very powerful wizards are allowed to run unchecked, then the battle can be turned quite swiftly, and dramatically. However, when the enemy forces always have teams of wizards working to subdue and blunt the effect of the other side's wizards, and also deploys special characters and teams designed to locate, identify, and defeat wizards, that tends to restrain some of the more awesome effects that a wizard, if left on his own, might effect. However, there are numerous things that wizards have to keep track of, all simulataneously, and the fantasy battlefield, at least against comparable forces, is not laying prostrate and helpless before the presence of one wizard or a thousand. In the flame and mass steel of battle, wizards, long after they have exhausted their spells, are eventually dragged down by armoured knights or warriors, often with war dogs or other savage beasts, and torn to pieces. Or, also fairly frequently, they are assaulted by teams of enemy wizards that hobble them or hammer them with a variety of spells that either kill them outright, or make it easier for other forces to reach them and kill them; or, oftentimes wizards are targetted with multiple spells of various kinds all simultaneously, along with several hundred arrows, as well as several dozen infantry, plus several other creatures or characters specially equipped to deal with fighting with mages.
In the end, in really large scale warfare between comparable forces, these things tend to blend together and restrain the more bizarre effects. This is true for example in many of the battles that the Vallorean Empire in my own campaign are currently involved in. The enemy forces have the resources, the ruthlessness, and the overall talent to at any given time, restrain much of the effect of battlefield wizardry, in a similar fashion and manner that the Valloreans have numerous wizard resources to both protect the bulk of their forces, and restrain the more severe effects of enemy wizards.
I suppose that would be my answer to your question Reapersaurus. I'm not sure why you allude to myself being "biased" towards one kind of response or another. It is merely a logical extension and application of the rules, with a few world assumptions, which are then allowed to run their course to the reasonable extent and broad effect.
Semper Fidelis,
SHARK