so my thoughts...i have read till a certain point...i would like to point out that i am also (trying to) doing a system of my own and i find we have some similar ideas on some topics so i will write down on what i (dis)-agree and how i have done it!

i totally agree that you shouldnt remove versatility from mages and that the power of some spells is the main problem and what should be addressed!
and i agree again about AC and how it should progress somehow depending on your class and your level and maybe from your race for monsters but not pcs!

"Epic Levels and Deities and Demigods" do you really have to do that? epic levels are like broken beyond broken in the original state of the game! shouldnt you focus on whats more realistically playable right now and once you have finished like 90% of the game you can do that?! same goes for psionics for me but thats personal taste!

magic items, personally i am of the opinion that items that grant you bonuses to your main ability scores shouldnt even exist!
In my setting i justify this by saying "the gods wish to show mortals that life is a hardship and you should strive on your own about improving it blaaa blaaa" in game mechanics,2 reasons:
a) an item that gives bonus to an ability score is a bit like metagming imo
b) the effect those bonuses have look at it this way,the effect on the char sheet is immense! a +2 to str goes to attacks,damage,so many skills and carrying capacity! its effect is huge! you can have so many different items to boost specific aspects but your mains shouldnt be able to change with magic items! (but i have no problem doing that with lvling)

spells: all and each one of them needs to be studied once again and changed and placed in the right spell level.

races: in my campaign, like in normal dnd, dwarves and elves once ruled the world. humans are the newcomers!but orcs are the rulers of the world! (Midnight campaign setting pretty much-what if sauron had won)
so since this was the idea...i was like "what made elves and dwarves the rulers of the world some hundread of years back and now what has changed?" so i decided that older races should get some really good bonuses and abilites according to their theme.
Like a dwarf would no matter what class be good at a stone-themed ability and weaponsmithing
while elves were always better with magic than all other races!
humans should be the most adaptable of all races while orcs the brutes!

classes: the biggest overhaul should go into classes...pretty much no class should stay as it is now and especially the fighter who pretty much doesnt exist anymore but he has become like you have suggested here an archetype! in dnd 2.0 there was the fighing-man, thats the name of my archetype for all sub-fighter classes later on which like you have done they all share some very common traits like HD and BAB! (dont know if we both saw this from somewhere or it just so happened we both had the same idea)
the bard is a prestige and the monk doesnt exist in my campaign!the only monk i know is this guy
chinesse,japanesse and other cr..p dont belong in my campaign! thats personal taste again!

multiclassing should come later on after having made some good drafts of at least a few classes. and its tough!

feats: i dont know how you have made feats since you have not made classes yet! cause the numbers behind feats should come in some agreement with the numbers you are gonna put from the classes and depending on how powerful all classes in the end are going to be there is going to be some connection with your feats i believe!

skills: classes like the ranger and rogue who are preety much skillmonkeys should be made 1st again i believe then after you have found a basic theme for them, you should make skills, which should all be of some importantce in the game...not like now!
also DCs need overhaul cause after 8th level there is no need to put ranks almost anywhere!
about a skill specifically Diplomacy have you read this?

magic items: i like the idea of minor,Moderate,Major etc...i think i will surely steal that from you!

spellcasting: its one of the most major overhauls in the game and personally i really love this idea, even though i have not playtested it yet and i dont know if it needs any tweaking for my taste, the idea behind it,is exactly what i wanted from spellcasting! but even if it needs some tweaking the guy has done an amazing job!

i am not sure i contributed a lot but its still better than "hey do you have a pdf for that?"