My problem with the 3e classes is the hard codiing of many class abilities. A good designed class, imo, lays the basic foundation (e.g, BAB, Save Bonuses, Skill Points, and skill choices but keeps things general so that the player and DM can take the class into different directions rather than prescribing specific abilities unless they truly are necessary to the class (e.g., spellcasting and spell lists for spellcasters and tracking for rangers, sensing and turn/rebuke spirits for a shaman). Otherwise, abilities should be left open to tailor with bonus feat choices and specialize further with additional feats and PrCs.
The fighter is one example of how I like classes designed. So, is AEG's Myrmidon by Mike Mearls despite being horribly named. The class is a warrior mage class gets spells, decent armor, BAB and hit die, but gets bonus feat choices every so often rather than forcing the designer's idea of some cool ability ( for example channeling a spell through a sword, on the player and DM setting. Now, there is nothing wrong with channeling spells through a sword, but that decision is, imo, a player and setting decison and, therefore, better handled as a feat with additional feats or a prestige class to specialize.
This is why, I dislike most of the 3e core classes as written and like the customizing a character (PHB) and Unearthed Arcana style class variants. Rage, Sneak Attack, Precise Strike, Sudden Strike, Favored Enemy- all of these should have been feats that anyone should be able to take, and bonus feats for there respective classes.
Rage: What limits this to a wilderness warrior? There are examples in myth and other stories of characters from more urban or civilized socieities that rage.
Turn Undead: Arent' there examples of non-priests, who just happen to do this through their conviction of faith? Iam thinking of the classic situation of the vampire telling the hero or victim, "You must have faith for that to work against me). Also, in setting where deities have their own portfolios, why is turn/rebuke given to every cleric. And what about settings without undead?
Don't get me wrong, I think a cleric of an appropriate deity should have this ability. I just don't it is an appropriate ability for all clerics or that it should be limited to only clerics when people of the appropriate faith should be able to learn this to represent their strength of faith.
Animal Companion: Why does every ranger or druid need an Animal Companion? It's fine as an option, but not something that should be hard coded into the class. The same for the Paladin's mount.
Sneak Attack, Precise Strike, Sudden Strike: Why should someone have to be a particular class to make a sneak attack, precise strike or sudden strike? Sneak Attack seems like something anyone can learn. Precise Strike and Sudden strike also seem appropriate to those trained for combat with the right weapon or appropriate style making it approriate for warrior types.
The Monk abiltities after level 5 are too specific for every setting. They sound more like prestige class abilities.
Duskblade's Channel: Why is it necessary for duskblades to channel through their weapons? That to me should have been a feat and something that wizards and sorcerers should also be to do through a staff. And, if a warrior mage type of character wants to focus their schtick on this, to me it is better done through feats or a prc. The designers, imo, would have better to have gone with a more general approach as per AEG's Myrmidon.