Here's the original context:
"the most powerful way to disprove that is to play a C.o.D. (Cleric or Druid). Noncore material will not be necessary unless you are going for pure overkill (Draconic Wildshape? Divine Metamagic?)."
Draconic Wildshape is actually quite balanced. You can't get it until level 12, it limits you to small and medium dragons, and so on. It gives some versatility, but by that point the breath attacks are pretty sad. Even the Reserve feats are outdamaging them. As for Divine Metamagic, it's not broken. Persistent Spell is. It's a common misconception.
As for the things that I find wrong:
-Takes too long to build a classed NPC, it'd be nice to just have books full of different premade builds for each class and each level. I'd pay handsomely for that.
-Grapple rules aren't complicated enough. Yeah, you heard me. It's too simplified. I want specific rules for side-guard pinning, and joint locks, arm bars, rules for chokes that cut off bloodflow versus airflow... Really, I'm just very sad ToB didn't make a grappling focused discipline to cover these things.
-There's no built-in hindrance to make casters think twice about spell dumping their heaviest hitters right away. I'd like some kind of rule to force them to wait till later rounds to use higher level spells (same for psionics and intiators) or something, to balance fights more, as well as make them more cinematic, where the big guns are saved for the final blow.
-I hate all spells that make a skill obsolete. Any such spell should add CL bonus to the check and let the recipient count as being trained in the skill, if it matters. So, Charm Person would add to Diplomacy, Knock would make the caster about as good as a Rogue at lockpicking, etc...
-Save or Dies. These were a sacred cow that needed to be killed. I'm trying to make a version where it instead leaves the person at -9 and bleeding, so if he has allies, they have a chance to save him, but keep finding technical problems in making it actually work as intended.
-Reliance on magic items, especially by the people who can't cast magic. There's now rules like dragonscale husk, VoP, and so on, but there should be more ways to escape the problem. That said, I like the wealth of options and items available. Reading MIC literally made me feel like the main guy from Duck Tales, diving into a giant pile of gold coins, feeling giddy. Probably the best thing to do is just accept standard D&D is magic item heavy, and make houserules for the occasional low-magic game.
-Random stat rolls and hp. This is one thing 4E did right, and I've advocated static numbers for these hugely important figures to my friends for years to no avail. Point buy should be the standard option, not rolling. It may seem small, but when faced with a DM insistent on using rolling, you have a better arguing position to also allow point buy if it's HIM who's trying to use the houserule. I'm sick of feeling helpless in new games to the DM's whim of rolling, knowing I'll probably get poor results that make my character concept impossible.
-Odd stats aren't worth




! There's no reason for this. You could make all opposed ability checks add score instead of modifier, for starters. Also, I believe the current rules are for any opposed roll (and initiative): higher mod wins, if the modifers are the same, reroll. Why not, if modifiers are the same, check to see if one has a higher score in the corresponding ability, and only after THAT reroll? It's little things, but there's no reason not to incorporate them.
-Flanking isn't harsh enough. A +2 to hit is pretty trivial, considering how bad it is to be surrounded. It's nasty with Rogues, sure, but I think the general benefit should be increased a bit. Not sure how, though.
-Monster stuff such as how much natural armor they get at a given CR is way too random, with no real rhyme or reason. Which makes it a pain to design new ones.
-Races should get to choose favored class from a list. Just one option is too limiting, and it'd be nice to get some non-core classes as favored options.
-Spellcasting prestige classes fell into two categories: full casting progression and no reason not to take, and not full casting / crazy prereqs and never worth taking, with no middle ground.
-Severe racial imbalance. Humans and Dwarves just blow the rest out of the water, and the half races are beyond useless.
There's more, that's just all I can think of right now. Despite that large list, most of those are easily fixable, unlike those with any other edition of the game, all of which would also comprise a much longer list of issues.