1) That doesn't address simple problems like Save or Die/Save or Suck. If your response to "He casts Hold Person" is "Well an enemy mage can cast that too", well great. But that means that it's mage on mage, and party fighter is left out. Or rather, he just winds up getting hit with various Save or Die effects while trying to stab the enemy wizard/deal with summoned monsters.
2) Do you see exactly how much effort you have to put into countering spellcasting? You need an intelligent organization who has far reaching capabilities, the capacity to watch the PCs and instigate plans just to address one or two classes? All the time. Not every foe the PCs will face will be uber-intelligent and prepared.
Furthermore, super-smart/capable enemy completely neglects situations where it doesn't work. Ok, the PCs bust into a crypt filled with undead and other monsters, and they bring the big nasty spells. So, what do the enemies do? Their reach doesn't extend further past the dungeon. Or take "Against the Giants" as an example. It's a long string of big brutes. How exactly do they deal with high powered spells - send giants out to watch the PCs and then hire wizards to deal with them?
If I have a choice been "10x the work just to counter the capabilities of high level casters" and "A system that's balanced so that I don't have to deal with that crap", I'm going to go with the latter and not sweat it.
I don't put effort into countering spellcasting. I just try and make scenarios that challenge my groups with or without casters. Your hold person example is a good one. If the mage is using those spells they will be very powerful at the levels in which that is their highest slot, and thats cool, I want my wizards to feel powerful. But if you design an encounter that only has one or two bads and your wizard trumps it and then you provide an easy mechanism for them to rest and do it again then the game is being paced poorly. Save DCs scale so at high levels that 1st to 2nd level becomes less effective.
You also have to take into account that magic in 3.x is one of the few actions that has multiple ways to FAIL. Spells provoke attacks of opportunity and can be interrupted with damage, spells can be countered, spells can be thwarted with magic resistance, creatures can pass their saving throws against spells. No matter how great a wizard is unless your cheesing with some with the old haste rules or some of the latter books action economy sillyness the mage only ever gets to cast one spell a round. Spells have material components.
I have seen some cheese with 3.x summoners, but that is one of the few cases where my group had to step up and make a houserule limiting the amount of summons the character could use simultaneously. And TBH it had more to do with the player taking too long on their turn then it did the actual spells. But then we do that to everyone. When a players turn comes up they are expected to have an idea of what it is they would like to do, they should have their spell looked up (or feat or whatever).
As far as the point I made about the enemy mages having magic as well. It does not usually end up being "mage on mage" in my games. In fact I would go so far to say that when an encounter comes up my parties almost invariably go after the casters first. There could be 10 other combatants and my groups will always try and deal with the mage first and foremost. This has been pretty much universal for most of the groups I have played with. The point I was making about the enemies having the spells as well was a party vs. monsters point. If your group has SOD/S and they are using them then why wouldn't enemy casters use them as well? Magic is a wild card and in a world where magic is present, then your mages are in terrible danger. Meaning that if the bombs they can drop arent enough to kill all opposition that they will face a great deal more aggro than the rest of the group. They end up using some of their spells to buff themselves or mitigate threats.
Mage on mage is kind of a classic fantasy theme as well if you look at it. Who better to deal with an enemy caster than your own groups magic specialist? But I guess in the end that is a playstyle choice and not a question of rules. If you don't like it who I am I to tell you what is fun for you. But on the other side of the same coin is the idea that in the games my group enjoys that its totally cool for the the gorups mage to go into counterspell mode and try and keep an enemy caster locked down while the rest of the group wades through the battlefield to try and eliminate the caster.
As far as the organization bit. It does not take an evil far reaching organization to have a tracker, or use some divination magic to locate the group. If your heroes are known (which I am assuming if they are receiving rewards from local leaders and helping out folks in general that they are known) then it becomes even easier to find them. Maybe they drink in the same bar every night or have a keep. It should not be any easier for your players to find a remote lair of an enemy as it is for that enemy to have a crack at finding the players home base.
In the end a wizard has some really cool toys, but they come with strings and balancing mechanisms, if you choose to let wizards have all the great toys and do not employ any of the balancing mechanisms or strum any of the strings that limit them, then of course they are better than anything else. Thats like letting your fighters loose and not applying DR or tracking HP.
But in the end its really a playstyle and pacing argument. In a game like 4e everyone is a wizard so the same kind of pacing issues effect it to lesser degree. If you choose to set up an environment whereby characters with daily resources can replenish them with no difficulty then is it really the fault of the system or the players? Design your world to be more resilient to metagame cheese. Storytelling games are a collaboration, it is the Dms job to challenge and the players and reward them for overcoming challenges.
And BTW the real bad guys in against the giants are drow elves not giants. If I am a drow elf using giants as pawns and some group is coming each day and killing a handful of giants with magic and coming back the next day and repeating the process, I have to imagine that after a day or two im gonna send in some of my magically resistant drow pals to deal with the 15 minute threat, or using some of the divination magic that my drow deity gives to find out where they are running off to and killing them in the night. But maybe I read the modules and missed the part where the evil clerics running the show would be cool with some random group whittling down their numbers one encounter at a time and they they would just wait for this force to get to them eventually after many many 15 minute sessions.
Its not 10 x the work to read all of the modules you plan to run and see that there are clerics involved and drop in a cleric or two or some drow warriors to challenge the group. Its just trying to let the enemies not be autonomous sacks of HP and GP waiting there to be slaughtered. I assume my bad guys (and girls) actually want to win. And letting a group come in and use the exact same tactic over and over again to wear them down over a very long period of time is just silly. If you had some bad guys attack a keep your players maintained and they came in with spells and killed a few guards and left, and started doing it every day, I bet your players could devise a plan in just a few short minutes that would have a real good shot at stopping the threat in its tracks. And your players consist of a group of 3-8 individuals of random backgrounds. Give the monsters a chance to act logically as well.
Sorry for the long post and thanks for the banter.
love,
malkav