Regarding Rule 002: The intent here isn't "common houserules"...it's to say that nowhere along the line was there an intent that you can make a spell LOWER level by ADDING metamagic to it. I know this particular rules loophole is popular...and sadly, that popularity means it's likely to not pass a general consensus muster, but I stand by both the rule and the reasoning behind it.
Regarding Rule 003: It's not a question of whether or not it "isn't even overpowered". In fact, some of these (see #4) are intended to correct unnecessary weakening of abilities through obscure corner-cases. I just genuinely believe that a class's features aren't intended to be exptended beyond the actual levels of the class...and the cited example is a pretty gross example of that.
I didn't narrow it down to just the specific class (both abusing and abused) because my resources to research the issue are limited...I don't know how many other short clases have desirable extensible features, and how many other "+class features" classes exist. The principle itself is sound and logical, I can't think of a good reason to have exceptions.
Regardinr Rule 005: Minor reword...sorry to de-humor it, but I can just see someone working in some bizarre ability that lets you do something whenever you're also taking a full round action.
Regarding Rule 006: Hopefully, you guys are ok with my rewording. It's pretty general, but I can't think of a reason why it shouldn't be. The concept is universal (and obvioiusly, I'm for it).
Regarding Rule 007: I'm also for this...added a bit for clarification. I'm presuming your intent wasn't to allow bite, gore, or wing slap attacks during a trample.
Regarding Rule 008: My take on this is that this is specifically aimed at Sorcerers. The subsequent feats also have Sorcerer level requirements, the feats nearly all relate to arcane casting...I read it as something intended specifically for the sorceror class, the class that "gains its powers from a hint of draconic ancestry".
I know it's hard to explain the distinction, as I'd probably allow this to stand as a house rule if one of my players asked it...but I can't honestly say that intent and common sense dictates this rule.
Regarding Rule 009: Regular clothing is considered +0/No max dex/no penalty/no ACF armor for the purpose of adding things to it (such as the Magic Vestment spell). In light of this, I don't see why padded armor needs to be made "not armor". Something has to be the lightest form of armor, it's described and established as such in that role, and yes...bulky quilted layers of cloth are (ever so slightly) harder to move around in than a regular t-shirt. I think it's clear that Padded armor was intended to be armor, even if just barely.