First of all this is a very good job its all very detailed and though I don't agree in certain places I would play with these rules, at least out of curiosity.

Also it depends what you mean with complexity. You rules are quite a lot but this is only natural if you want to fix specific problems. They also have the benefit, aside from removing many classes, that they don't change the game a lot.

My main problem with your rules is that you base a lot of your fixes on tiers. I am not very familiar with the reason each class goes to each tier but as far as I understand tiers are granted based on a class used to the maximum (infinite loops and pun pun not withstanding).
Say anything you want about the cleric being op but at least you get a perk for being delegated to healing. Unless I am mistaken in your rules someone will have to pick a Healer or a water/gentle way Shugenja and I can easily see a situation where no one wants to do that, though tbh this can also happen in normal games.
So in not high op games the healer/warmage may wonder why the dungeoncrasher, zentarim soldier fighter is getting all those extra feats, ability increases and iterative attack and he gets nothing. But maybe that because I never cared for optimizing a healer or warmage and I just played a cleric or wizard.
Tier 5 classes end up with +15 to an ability and +28 feats compared to the base line.
Tier 4 classes end up with +10 to an ability and +19 feats.
I can see this being overkill and many games. On the other side if you play with an optimal way this could be a good solution. Again a lot of this is pushing the game to the point where tiers matter.
I am considering a fighter 20 will be better than a warblade 20 with these rules. But again I don't remember how much you twink the warblade.
I guess you could advise new player to pick classes from the lower tears.
This also makes prestige classes very hard to use as the DM will have to assign tiers to each one.

Random question but is there any way to access teleportation in your rules? Psionics propably?

Other issues:

"Magic and mundane items that are uncommon or difficult to make (either in the region or everywhere) have a higher effective price for determining whether a community of a certain size has it available to sell. "

I am curious in how this helps with balance or why its needed.

"The first encounter in a day has only 50% XP, the second 75% XP, the third 100%, the fourth 125%, etc. This is a solution for the problem of the 15 minute adventuring day by providing an incentive to have multiple encounters and conserve resources rather than using all resources then waiting for the next day to arrive. "

I really like this I have my own modifications to xp per encounter. A problem I see with your version is that the turn of the encounters can change the xp you gain. Facing CR9, CR10, CR11 is different xp from CR 11, CR 10, CR 9. But maybe this is intentional?

What's the reasoning for the Hide and Move silently rules? Asking because I am genuinely interested.

The rule that removes spellcasting from creatures and also advices to change their CR is a bit prolbematic IMO. I could see it being hard/too much work modyfying those CR's. How about replacing the lost caster levels with Shugenja ones?

Iterative attacks seem overkill to me. I wonder if how the warblade compares to the fighter with the rules you use. I mean fighter already has dungeoncrasher and zentarim soldier. Your rules are also an indirect nerf to the monk and standard action attack manuevers. Maybe allow the monk to add flurry attacks to the standard action attack?

I am not sure how to feel about critical effects stacking. Doesn't this makes crit fishing even more obnoxious?

Double con score to death is interesting. I use level+con score. I think I also like the you are disabled part. Is it to avoid getting coup de graced and having the option to just nope out of the combat?
The armor UA rule is interesting, also goes toward making the already petty lethal dnd combat, less so. It is however sth that increases the complexity of the game, though sligtly above the level dr does.

The fear change is also nice.

Also is dragon magazine allowed? I am not very familiar with it or actually know any of the lower tiered classed from it.

Regarding the ban list, are Splitting arrows allowed?