If not the biggest problem, just say all the problems you can think of. I'll begin this thread by saying a few that I've heard around (Most of what I say here is about the wizard, but this thread is by no means limited to the wizard):
[*]Scrolls are too cheap by the rulebooks. Thanks to this cheapness, the Wizard (and Sorcerer too) can amass such a horde of scrolls with their enormous disposable income (Not really needing weapons or armor like most other classes do), and will always have something that can resolve the encounter/situation without really any effort.
[*]Utility Spells like Invisibility and Fly last too long.
I wouldn't list those last two spells as "utility". They're OP due to their defensive potentially, especially invisibility.
In fact, I find invisibility to be uniquely broken (compared to 4e), the issue not being the spell so much as the rules around perception, stealth and blindness. In 3.x, invisibility is "real" invisibility, in that you get no visual indication of where the target is. Invisibility gives a +20 bonus to combat Stealth (and potentially higher bonuses outside of combat), plus there's an irritating minigame revolving around finding which square an enemy is hiding in with your ears, then attacking that square with a 50% miss chance due to total concealment, and potentially wasting a round sticking your hands into two adjacent squares... Being blind is also one of the nastiest conditions in 3.x.
In 4e this is vastly simpler. Blindness isn't really blindness (it's blurred vision), and invisibility isn't really invisibility (it's total concealment, period). Being invisible gives you no numerical bonus to Stealth at all. What it does is let you hide in plain sight.
If you fail your Stealth check, your opponent knows where you are, and can take the -5 penalty to hit you. Significant, especially given how tight 4e math is, but not unstoppable. If you make your Stealth check, then your opponent has to guess where you are. First you make a Stealth check against passive Perception, then if you succeed each opponent can make a Perception check as a minor action to try to find you (if there's line of sight, which is kind of a funny concept considering they can't see you).
In 4e, flying is simply far more limited, at least when it comes to being given to magic-using PCs. (Monsters that fly are pretty common.)
Otherwise, some other consensus I received was that if the GM were to enforce Spell Components, such as Material Components, Focuses, XP, and others, then a lot of issues that people have with the wizard will likely become a lot less of an issue.
I disagree. I think those are artificial and unfun fixes, plus they require tedious record-keeping. I think the issue was a lot of poorly-balanced spells. Many of these spells appeared in 4e and are balanced, requiring few fixes.
One issue is duration. Rituals were a good fix in 4e; you want a long-term benefit? Then spend a long time! (Alas, they were usually too expensive, at least at low-levels when people would learn to like them, so by epic when they were cheap noone was using them.)
for example, the Transform spell, which is a 9th level spell, requires a Jade Circlet thats worth up to 10,000gp. Yes, its only 10,000gp, but lets also ask, who in the world will be keeping such high quality jade circlets around? A D&D equivalent to Bill Gates with an eccentric fashion sense? A few powerful wizards, and even then, how many exactly?
I'd be more concerned if I found Transform to be a "broken" spell, which I don't find it to be. I don't like "screwing over" players by denying them their rightful tools.
If I think a spell is broken, I would rather ban or nerf it than use such an artificial unfun "balancing" technique.
Though I am sure there are others. What more is it about spellcasters like Clerics, Druids, and Wizards that make them so powerful on their own?
One thing is save DCs. Save DCs scale at the same rate as a good save (and sometimes faster, if the good save's stat isn't being boosted every four levels; for instance, a fighter isn't likely to boost their Constitution organically) and far faster than a weak save. It's usually pretty easy to guess someone's poor save. The big guy in clunky armor isn't moving too swiftly, so you should cast Otiluke's Resilient Sphere (a Reflex save targeting spell) at him. That guy is going to be locked up for 1 minute/level (minimum 7 levels) and doesn't have the tools to get out. In one round, you just took out an opponent with a single spell, for the entire combat. That started out being about mismatched save DCs, but note the duration issue too. (In 4e, such a spell typically gives a save per round, with a flat 55% chance of making it; fortunately, 4e also fixes another end of the equation, in that the wizard always has something to do
every round.)
A few sessions ago in Kingmaker (it's Pathfinder, but pretty similar to 3.x), we ran into one of the same issues that breaks 3.x magic.
The DM is allowing a fairly high point buy. (3.0 was playtested with 25 point buy, with wizards starting with Int 15. Naturally, none of the starting races had mental stat boosts.) We had a new character, an elf "necromancer", and he started with natural Int of 20 at 1st-level! (He was 8th or 9th-level, so he had an Int of 22, before his +4 headband of intellect.) Being an elf, he got +2 Int, and the point buy was so high he could start with an Int of 18 before racial mods and still not have terrible Dex and Con scores either.
He could throw around spells with save DC of 18 + spell level, so a max of 22. We're not facing too many 8th-level opponents with a weak save of anything like +12. He used Hideous Laughter on an opponent, and said opponent could save each round (much like in 4e), but the save was a full-round action, and the save DC was so high he wouldn't make it, so it wasn't much better than Otiluke's Resilient Sphere.
And then I found out that Mirror Image, a powerful but well-designed defensive spell, got beefed in Pathfinder so it's now ludicrous... I used to detail that spell's great design potential (it doesn't bother trying to boost a wizard's weak AC and hit points, but at the same time a non-caster can get through the images by making multiple attacks, which of course means the wizard survives a while longer...) but Mirror Image in Pathfinder uses the caster's AC, which
can be buffed to the point that attackers start missing images
So I think high stats are a problem too. I seriously doubt anyone plays 25 point buy D&D, and even if they do, who actually plays a wizard with a starting Int of only 15, other than the original playtesters? (I doubt Int 20 casters at 1st-level are an actual problem in 3.x most of the time, but you could get a save DC this high with Spell Focus and some non-core feats.)
In that same encounter, the DM was far too permissive about us buffing. I play a druid, who benefited considerably from buffing (before he got a Belt of Giant Strength anyway; prior to that battle, my own druid used Barkskin and Bull's Strength, along with hour-long buffs such as Wildshape, Greater Magic Fang and Longstrider), and the barbarian/alchemist could use Enlarge Person and his mutagen, etc. This is both a rule and a DMing issue. In 4e, buff spells only last a round (but are often at-will, working on an attack spell, or are a minor action), meaning you can't just buff to the gills, increase your power level by 50% or whatever, and then blenderize the opposition. That's the kind of thing that divides fanbases though.
There's more. Last session I think I might have broken an encounter with my druid. In Pathfinder, wildshape is much more balanced (though a lack of playtesting seems to have resulted in wildshape giving poor armor class scores unless the DM is as nice as mine). Wildshape wasn't what broke the encounter. Having just reached 9th-level the druid summoned a Large air elemental with Summon Nature's Ally V. (Because of the the way wildshape works, forcing you to actually boost your Strength, unlike in 3.x, where a Strength 8 druid was still a terror while wildshaped) my druid boosted Strength rather than Wisdom. So his save DCs are low, and he has few bonus levels, and no bonus 5th-level spell.
Still, what I could do with that spell is frightening. I summoned an air elemental, which then turned into a whirlwind, with save DC 18 to pick up opponents and move at 100 feet per move action. (The whirlwind doesn't have to attack, it just needs to touch or move through an opponent, helpfully not provoking attacks of opportunity.)
Oh, my druid has Augment Summoning, which boosted the save DC to 20 (+4 Strength to summoned creatures, and the save DC of the whirlwind is Strength-based).
The rules were poorly written too. I'm not sure how many saves a victim gets when first hit. Can they only get sucked up if they fail two saves, and not just one?
As it was, my elemental turned into a whirlwind (standard action), then literally swept the battlefield, attacking all five enemies (it's Large, and has a fly speed of 100). Three failed their saves and got transported away. One round later and they were too far away to do anything, plus one was nearly dead and had turned into red goop. Next time I'll have the elemental go straight upward, so that killing it from the inside becomes a bad choice. (Of course, not killing it is a bad choice to...)
And the next turn, while two creatures were essentially Otiluke's Resilient Sphered, my druid got to fight as a bear, and his animal companion got to fight... you can see why druids might seem OP there.
At no point did my druid have to spend a single material component or anything like that. All I had to do was be more than 5 feet away from potential attackers (easy when a Huge bear has so much reach, and I can literally have my druid be in bear form all day).