I agree with:
Rule 1: Drowning is drowning. The fact that it reduces your health to 0, by RAW, was clearly not intended to increase your health.
Rule 2: Again, technically RAW-legal (and I have done this to create a fiery empowered Orb of Cold as a level 4 spell; I quit before going higher levels), but it should never have been.
Rule 5: Dead is dead.
Rule 6: Monks aren't proficient with unarmed strikes because they... Aren't proficient with simple weapons? Yeah, sure, OK, roll to punch things with your fists at -4. Makes perfect sense.

I disagree with:
Rule 3: Forgive me if I'm reading this wrong (it's early and I'm weary), but doesn't this explicitly state that no class can have its features advanced beyond 20 unless specific mention was made of them? That seems very awkward, as it's going to boil down to what book the class was printed in, as opposed to the actual merits of the class features being advanced. (There are epic progressions for Barbarian through Rogue; are there any for Knight, Factotum, Scout, or Dragon Shaman? Common sense dictates that the Fighting Challenge/Shield Block features of the Knight, Inspiration progression of the Factotum, Skirmish, bonus feat and perhaps battle fortitude progressions of the Scout, and breath, aura and natural armor progressions of the Dragon Shaman, respectively, should naturally progress to epic levels, but (and unless I'm missing something; I'm not too familiar with the epic rules) they won't because specific mention was not made of them, which seems contrary.
Rule 7:
Trampling with paws doesn't make sense. Nor, for that matter, does trampling with unarmed strike (which is what a human with trample, which can happen with the right feats/maneuvers/spells, though I can't recall how, would do). A monk steps on you harder? This feat should instead have "prerequisite: hooves (4)".
Rule 9:
Padded armor is, in fact, distinct from heavy clothing. A fitting modern-day comparison might be the difference between the armor padding that fencers and other swordsman (such as those practicing kendo) have to use, vs.... Heavy clothing.

Further, I maintain that it makes no sense for clothing to ever have an armor bonus. +5 loincloth makes a lot less sense than counting padded armor (which is historically a thing that exists) as armor.

I don't understand the implications of:
Rule 4: What's the difference between this and what we have now? Somebody has to spell this out for me.
Rule 8: Isn't there already a feat that does this? Or am I misremembering?