I see it as an attempt to solve problems that didn't actually exist. It seems to me that the 2 radical moves it makes are to make investigation 'nonrandom' and to remove the stats for the big baddies.
Let me take the second point first: removing stats for the big baddies. Let's recall first of all that in the central story of the so-called Cthulhu Mythos, "The Call of Cthulhu", Cthulhu is defeated by a mariner who rams his boat into Cthulhu's noggin. So much for the oft-repeated gamer myth that when a Great Old One shows up, d100000000 investigators automatically die and the rest have their faces spontaneously explode for eleventy-billion damage. You can (at least temporarily) stave off the end of the planet with the African Queen, and you don't even need Bogie to do it. But how does anyone know that if the squid doesn't have any stats? Then it's just pure fiat.
This applies to other things that investigators might try in the game. If they somehow mess up and the cultists get their ritual completed, the Keeper doesn't have to say "Well, OK then, the faces of all human beings spontaneously explode. The end." There might be something you can do to take out the monster. And the different monsters are different, not only in their "story hooks" but in their attributes. That's part of the game.
This also leads to another issue with the way people look at the Mythos. It seems that a lot of gamers seem to conceive of the Mythos as a regular pantheon, with invincible entities that are always one step ahead of mankind and are made of Teflon (evil Teflon, but still). However, I think the point of the Mythos is that these are just alien beings of immense power. Sure they're (mostly) big, tough and psychic. Sure some dummies worship them because they don't know what they're really dealing with (and thus end up consumed). But they're not really gods. They're just giant, hungry aliens with psychic emanations strong enough to melt you.
In a sense, gamers have tried to turn the Mythos entities into Mary Sues. But really they're just big monsters that can get unlucky or have a bad day in the material universe just like anybody else.
As an aside, I had this same problem with Cloverfield: you're hitting this thing with 2,000lb bunker busters and you don't even scratch it? I call B.S. The monster already has enough advantages without the screenwriter having to cheat on its behalf.
The other issue was with the investigations. Sure, there are a lot of times when a helpful clue requires a Library Use check to turn up. There are a couple of points with this. In a well-written adventure, the solution of the adventure should not turn upon a single clue. Now, in an especially tough adventure, there might be one clue that gives the players a handle on the most elegant and complete solution, which they would otherwise have to conclude to from disparate sources. However, the adventure can be completed with relative success (like, you can survive it) without this clue.
Further, clues are often available without a skill roll; it's just a matter of checking for the right information. I ran a Modern scenario (in a sort of proto-Delta Green game) where the PCs should have checked to see if an agency tracked the entrance of an unidentified meteor-type object into the atmosphere, but they neglected to check up on that sort of info and so missed a clue. But the point there is not to punish them for not guessing right on a blind guess, but to punish them for not being thorough. That's the point of the investigation, to me: can you be relatively thorough in the given time with the given resources. Obviously a contest of "guessing right" is no game at all, it's just silly.
Likewise, clues that are available with skill rolls, especially Library Use (the most common one in my experience) do not become unavailable if you missed the roll. There's a game to that, too. The Keeper rolls the check secretly and then announces "After 4 hours of research, you don't find anything relevant". The player then gets to make a game choice: keep going, in case it was a failed roll, or spend time on something else? And maybe they are up against the clock, or maybe they are not; they may or may not even know. So it's a real choice that the player is making. Maybe the PC will stay for another few hours; maybe that will be profitable or not.
Of course, having a low Library Use skill is as dangerous as having low combat skills and getting into lots of fights. You want to send your person who actually knows what he's doing to the library/archives, just like you send your combat guy into combat rather than johnny pencilneck.
So in my experience, the game doesn't really turn on a single Library Use roll, or even a series of such rolls, since you can generally just keep rolling. Also, if the party decides that it missed a clue at some point (like they find themselves lacking info) they can always send guys back to the library.
And finally, I find CoC to be a game of hard knocks and tough breaks anyway. You're really up against the "most dangerous game" in that one. Some times you get the bear, and sometimes the bear gets you. Especially when the bear is 50 feet tall. It has the same basic requirement as an old school dungeon crawl: you better bring your A game.
