1. It kinda has to be that way, unless you expect me to just hand out resources and break the whole concept of the gated progression that drives the pack.-snip-
2. This is a case of RTFM, the first Witchery Quest outright says that the witchery quests are split between changes and teaches.
3. This is due to the fact that there are two ways that you'll potentially get resources for the first time - Crops and Nether Ores. If I have it requiring the essence or the nether ores then the person who isn't the way the quests expect gets shafted and won't have the quests for things needing that resource unlock. In the past the seed quests were directly required rather than these trigger quests - this caused both the issue mentioned above, and also caused a lot of lag further into the quest book due to the huge number of nested progressive requirements a quest could have, hence the change.
4. There are few instances of this ever being a problem, but as far as I'm aware it only occurs with players choosing to advance through witchery without following the quests and making the books - See point 2.
5. 90% of the time people will have gotten gold and alumunium before getting redstone, so that's just a case of you fulfilling requirements in an unusual order.
6. The Nether stuff is there as a plot device for the theme of the pack and to act as an alternative means of resource acquisition for those potentially wanting a break from crops. The strict mining progression is there to match the crop progression.
7. NEI crashes are well known, and are a result of the way Minetweaker silently reloads scripts whenever you enter a world (even after just going to the title screen) and the fact that AE2 doesn't like recipes in its inscriber being reloaded as it caches them. Only way to avoid this currently is to relaunch the client every time you disconnect from a world - Annoying, but if you don't you'll crash as soon as you check any recipe anyway currently.
8. This is basically just a case of some scripts not loading properly upon a reload as I'm presuming your issue is specifically with iron ingots. For some reason there is no recipe to cast iron ingots in the ingot caster (@joshie I keep meaning to ask you why this is) so I add one with scripts, hence no iron ingot casting when that script doesn't load properly.
A lot of the stuff you've said in the subsequent paragraphs boils down to the pack still being alpha and me not having the time to work on it as much as many would like (life before minecraft, the usual deal). I do appreciate the feedback though and am appreciative that you've taken the time to go so in depth.