In order to make them equally powerful, the 3.X CoDzilla and wizard need seriously cutting back - and wizards shouldn't be able to do anything because "It's magic". And people are arguing against this.
I wont respond to most of your part of the statement because I havent gotten past the first couple of years of 4e, so I dont have much to refer to. But I would disagree that looking at both PHs the classes compare well for 4e. Its all from my point of view but in 3e the separate mechanics, the different ways things work from class to clas, the alignments, the different focuses on strengths, the fluff IN the text, all serve to make it something I would MUCH rather give to my players to create deeper PCs with. Thats just my opinion though.
As for CODzilla and the balance of 3e I would agree they were some problems, most of them are in my mind easy fixes without changing the structure of the class.
First I would remove scroll writing, and magic item creation, leave this up to a splat book or a DM. Or find some other way to do it so that a mage doesn't wander around with a chest of scrolls. This was beggin for a houserule in 3e.
Second any spell that makes a wizard a better fighter then a fighter needs to be removed or toned down, that include summoning and any type of transformations (I think Pathfinder did some work with this).
Third, I really like save or dies, they are an awesome part in an adventures, where the character tries something, and sometimes they work, but sometimes they dont. But I know there were builds that maximized your DC so that they always works. This needs to be fixed. I would think against a foe at equal level, a save or die, or save or blind type thing, the absolute MAX chance for success should be 50%. If the foe is lower level, it might go up but there needs to be some hard math work in making sure this isnt abused.
I'm less concerned about the fighter being a better rogue then a rogue, because the spells had to be memorized for this, and the wizard lost other power for it... but still it does encroach on the rogues area which could ruin some fun for a rogue player. In my campaign I solve this with magic being semi available, so the rogues dont worry about invisibility spell because they have a scroll if they wanted one. Still I could see some work toning this down a bit.
Other things I would include is:
-Spells fizling when they are hit, the concentration skill etc
-Spell book reliance, I like this traditional weakness of the class. Great story hooks and gives the fighter something to laugh at the wizard about while they search for his spellbook, (or while the wizard rebuilds his list). -Perhaps there can be some middle ground where the wizard remembers one per level or something, so that even if a spellbook is destroyed the wizard may still carry on. This may make the weakness useable in campaigns.
-memorizing spells. if you dont memorize the right spell you dont have it. and you must memorize all spells at rest
-adding the at will power (as an option) from 4e.
-Im of two minds of rituals. I like the intent, but I dont like the seperation in the book or in the game mechanics. I dont like them being accessible to every class, or how they are not really related to class spells/powers. I prefer all wizard spells being "spells". I would much prefer a mechanic for casting a "non combat spell in casting" E.g. this takes 3 rounds to cast, and your going to be vulnerable doing it. Having a way of saying that in the spell so that a wizard can still try it if they need to.
I also think some changes and options need to be brought to martial classes. 4e did well in this regard in many ways.