It might be an unpopular opinion, but I think the general aim to remove the "illogical" puzzles from adventure games may not necessarily be a good thing in and of itself. I think that there are definite subgenres where having all-logical puzzles works well: the Myst series, since those are mostly based upon "mechanical" puzzles, or a mystery set in more or less the real world, are good examples. But then you have games like Nord and Bert Couldn't Make Head Or Tail of It wouldn't work at all in that case, since it's world isn't trying to be immersive; it's just trying to be a very "game-y" place. (That might make it more of a puzzle game, but where adventure games end and puzzles begin is a difficult, separate topic.) Or a game set in a cartoon universe, where "cartoon logic" applies instead. Or, say, the King's Quest games, where clues come from fairy tales and such.
This is very different to what I (and others) were complaining about earlier with the pH thing. There (if the puzzle is as described, which it might not be and has just been translated poorly from the game) it's actually punishing you for extra knowledge: if you know how pH actually works, then it just breaks your brain when the puzzle (again, if it is as described) goes against that in such a spectacularly awful way; moreover, if you don't then you'll have a worse understanding of what pH is in the real world at the end of the game (and why, if you're going to use existing terms, use them properly or not at all). What I'm talking about is the exact opposite: rewarding the player for having extra knowledge by allowing them to make progress, even if it's with puzzles that aren't explicitly clued within the game, or require you to go outside of the game to figure them out. It's a bit like you and the developer are going head-to-head: both of you can use all the resources at your disposal, and whoever comes out on top is the victor of that battle of wits.
I guess what's brought this on has been thinking a lot about cryptic crosswords (another thing I enjoy doing sporadically). If you're not familiar, they're much like regular crosswords, only the clues are heavily word-play based (rather than strictly dictionary definition-based like regular crosswords) and that it usually helps to what the "rules" are before you start solving them (otherwise they'll just seem like gobbledygook, although a few are incredibly clever and can be both a "straight" and cryptic clue). However, if you're good at playing around with words and letters, and you have a good command of the language in which it's set, you get rewarded by completing a puzzle containing (hopefully) some very cleverly-constructed clues.
Another thing that's brought this on is that my husband got me a really great puzzle book for Christmas: it's called Maze by Christopher Manson (apparently there's also a game version of it). It was one of those "Figure it out first and win a prize!" deals. You're given very little direction, and very few specific clues for how to proceed. The whole thing can be incredibly overwhelming when you realize that anything and everything can be a clue. But a lot of the clues/references reward you for having knowledge (or at least, the ability to gain knowledge), and trying to put all of these clues together to figure out how to get through the maze, unlocking all of its mysteries.
Yet another (which I thought of mid-writing this post) was Dracula's Riddle: I think that's still up on the internet if you wanted to have a look. Again, it required you to put in a lot of effort and be crafty, especially if you wanted to work on it by yourself. But again, I felt like my own thinking improved by playing it and trying to see how damned clever the setters had been.
Now, this is very different from the cat mustaches and rubber duckies of this world, but I think that the baby's been thrown out with the bathwater, which is why story is now such an overwhelming force in a lot of new adventure/"adventure" games. Granted, maybe I'm just weirdly masochistic (I mean, I do play text adventures by writing my own maps and walkthroughs), but for fuck's sake there needs to be some better middle-ground between people like me and those who claim Myst is hard (which it is... but only if you happen to be deaf, or illiterate, or innumerate) where the latter, who don't want to be genre-savvy or be bothered looking up anything but a walkthrough, get to set the level of difficulty.
Also, as a separate note, if you like puzzles, I heartily recommend the movie The Last of Sheila. I won't say anything about it to avoid spoilers, but it was written by Stephen Sondheim and Anthony Perkins based on their own set of games with their friends. You'll even get something out of seeing it twice, because the movie is littered with clues. It also has James Coburn mockingly going "Boo hoo hoo!" at a young Ian McShane. Also Raquel Welch.