That seems like a whole 'nother can of worms. If we're talking about re-writing books, there's a lot more egregious stuff just in Core than the Tome of Magic.
I don't know what you mean. Monks are so OP they don't really need proficiency with their unarmed attacks on top of everything else they get.
/sarcasm
But ToM has entire systems that do not work, and require copious house-ruling in order to function in any remote way like what they were intended.
Core, for it's part has a lot of issues with it's ivory tower, but you can still have a decent game with those classes, even Monk. Even without house-rules, though house-rules can make things much more congruent.
Whereas Truenamer, a class I think of as being really cool in nature, and thoroughly rooted throughout the mythos of the settings since I can remember, doesn't work. At all. I keep looking at playing one, then remembering why I don't.
Shadowcasters got an unofficial buff from their designer.
And there are 10,000 homebrew fixes for everything. Monk, Truenamer, Shadowcaster, heck, the Wizard has a lot of debuffs.