Regarding Feats: I would recommend splitting the Feat list into a "Core List" and an "Expended List", even in the first draft. I only speak for myself, but if there's one person who mentions it, there are usually a lot more who are thinking it. And I would want to run an E6 game "Core only", that is, without the additional OGL material and only the very most neccessary new E6 feats. When core and non-core feats are all mixed up, it's very difficult to do that, and I would need to use a different SRD to get my "clean" Feat List.
So maybe a Feats I page for the core feats and a Feats II page for the non-core feats. I would hugely appreciate it, and I guess so would many others.
And there's something regarding metamagic feats: There are several feats that require a slot "3 levels higher". That would only be possible by picking 0 level spells and using 3rd level slots. And 0 level spells are always 1 target, 1 damage die. Something I just can't imagine anyone ever wanting to do, and even less anyone spending one of his prescious feats on such a barely useful ability. In my eyes, they are redundant.
If you really want to be as close to the rules as possible, they are still viable feats, but I would always remove them from my game. Just something to ponder, either way is fine with me.
And I havn't gone through the whole thread, but one problematic subject would be Monsters with Caster Levels. Some creatures have access to spells or spell-like abilities far above 3rd level and some even have access to complete spell lists.
Just that PCs are unable to learn these spells doesn't have to mean these spells are not existing for powerful outsiders. For the CR 16 Planetar alone, we would need the complete Cleric spell list. But for just two or three monsters, I wouldn't want to have all these spells in the E6 SRD. What to do about that?

Option A: Keep all the spells in, that could be learned by creatures. Really don't like it.
Option B: Remove all creatures that would have access to such spells. Since it's mostly high level outsiders that will show up rarely anyway, that's a slightly better pick, but still not a nice solution.
Option C-1: Crop all these monsters down to Caster Level 6th. This helps with some, but there are still lots of spell-like abilities.
Option C-2: Make a seperate list for spell-like abilities. But that's quite an amount of work.
Option D: Have a "Player Spell List" that only includes spells accessible by PCs. Have also an "Extenden Spell List" that is identical to the complete standard spell list, minus the ranger and paladin spells (as there are no creatures that use those).
These are just some options, I'm sure there are more. But I think going the very straight way is not a viable choice here. Either the spell description tripple in size with spells that will almost never be used, or we have to change something about the monster-section.