Actually I have made dozens of posts about this issue, but it seems you haven't read them. Oh, the irony

I tend to miss a lot of things, whoops

1- The idea behind pearl of wisdom is dumb. People want to play, not read.
The same applies to the docs as well. Not to say that having documentation is dumb by any stretch. Having background information is always welcome to have of course. Especially with D2, since just about every day I learn something weird on how it handles things. Hell, I still don't get how poison damage works sometimes.
My issue with Median, at least, comes from the requirement of reading them, for reasons I already explained.
2- Ubers are where they are due to limitations. Challenges work as they work due to limitations. This is plain obvious. A lot of content is not pretty due to limitations. Both laz and me had to offer content in ways that were not created in the most optimal way simply because we didn't have another choice. For example, anyone who thinks we stuck to the concept of heroic shields because we actually think the mechanism is fun and cool is just plain retarded. So is someone who tries to judge MXL from a "proper game design" perspective, really. Median XL is basically the medicine you give to your old grandma that was supposed to die 10 years ago. You cannot do this without inevitable (and many times irreversible) side effects (see: LC0 - was nice having you). If we want to talk about game design, let's grab a game where the developers actually have access to the game's source. I don't want to sound like a dick here but this is flat out the truth.
I do understand where you come from though. We have ubers where we are because there is no other place to put them. Heroics exist to 'simulate', in a pseudo manner, a boss with massive health, to compensate for the fact that caps exist for health. Median is probably one of the more innovative mods to push the game as far as it can, while keeping the installation involving a single file. It's flawed yes, but I feel like there could of been methods to work around the issues. Granted, now that I actually read your posts, considering where you can now place Ubers out of sight and mind, this is mostly irrelevant and it seems pointless to go on about potential solutions, because Sigma.
3- As for subtext to catalysts, oils, yadda yadda... Again not a great idea. How will you explain what a catalyst of disenchant does without explaining the whole concept of disenchanting and the benefits from it in the first place? Answer: the problem actually lies in the high amount of cube dependency there is throughout the game, not in the reagents having no description.
I agree with you on that. In cLoD, you get the cube for the first time. Cain tells you of it's possibilities, and what kind of recipes you can make with it. But the most relevant thing he tells you is how to upgrade games. That is it. The game never tells you any additional cube recipes, apart from cubing quest items in act 2 and act 3. Instead it incentives you to go look it up, and see what discoveries people made on what you can do with the cube. You don't get anything that at least drops a hint, or anything that encourages experimentation. No one in their right mind would say to themselves "what is I try this Helm, Perfect Ruby, Jewel, and Ral rune in the cube?" Or better, who in their right mind would consider throwing away their Stone of Jordan on a rare? Many of the cube recipes involve oddly convoluted and specific materials to be shoved together in the cube.
Same thing applies to runewords. Who the hell is gonna toss in random runes they found, when they cannot unsocket them, when you don't have any contextual clues on what sorts of combinations to use (apart from the barbarian mercenary trainer who hints you to put them in an order)?
Granted with Median, yea you couldn't explain every inch of detail without shoving a wall of text on something like oils of crafting now that you mention it. With that specific oil, it would be something like: "Cube with a jewel, arcane shard, X rune for this effect", times how many possibilities there are.
In the case of runes for Median, one may toss a gem or jewel into their weapon or armor at the start of the game. To their surprise, they notice that it only took one rune, gem or jewel to make a "runeword". But when they realize about an item having 2 sockets, it makes them ponder on why it didn't work this time. It either leads to experimentation, or just the knowledge that it, at bare minimum, takes only a socket to make a runeword. Alongside with the knowledge of the fact that one can unsocket a runeword, the only penalty it could lead to is some gold.