Simply put, the inherent flaw with Minecraft is that it's a game of discovery - but one in which the means of doing so are abstracted in such a way as to be occasionally unfathomable. There's no tutorial that teaches you how to build a furnace, nor the vagaries of the potion-brewing stand; no hint of direction that would even suggest a potion brewing stand was possible.
Many of the recipes and systems that Minecraft requires you to use are admittedly very sensible - place strings and sticks in a rudimentary bow shape on the crafting table and, presto! you've built yourself a bow. Other recipes create rolling chains of innovation; if you can build a pickaxe with this shape, can you build an axe with this one? Yes, you can.
Other items require larger leaps of logic, if only because the new endgame content increasingly pushes Minecraft in a direction you might not have anticipated. What starts off as Robinson Crusoe in Legoland ends up a tale of extra-dimensional travel against foes who teleport closer whenever you aren't looking. The result is that, if you aren't sitting with Minecraft Wiki open in the background, you can easily stumble into a dead-end. It's only the in-game achievements system that evens hints at the possibility of paths you haven't seen.
Image by SamJB2
At the same time though, finding out all this for yourself is part of the fun of playing Minecraft for a lot of people. The piles of blocks, the procedurally generated worlds, the multiplayer servers; these are essentially a giant question mark. What can you do today?
Ultimately, whether you look at Minecraft's lack of hand-holding as a problem or boon comes down to a matter of personal preference. Analysed with an objective critical eye, it has no huge positive or negative impact on the wider appeal because the game is consistent in this sandbox presentation of its world. It's merely a design choice that new players will need to understand and either accept or reject. A Lego kit isn't bad just because it doesn't show you every permutation of how the blocks can assemble.
Instead, what does have a lasting effect are the inconsistencies; the sudden introduction of inter-dimensional objectives, the inability to meaningfully customise your sandbox prior to jumping into it and the fact that constant updates may still create problems with the 'final' version. These are real problems with Minecraft, even if they haven't stopped four million people from buying the game already and aren't the reasons that Clive, Harry and others look down on the game.
Image by Zolamee
Honestly, we're not sure why gamers can be so easily divided into 'Likes Minecraft' and 'Doesn't Like Minecraft'. All the usual reasons that get thrown up by detractors are either quickly deflected or just as easily levelled at other games. Minecraft is no more or less pointless than any other game or form of digital entertainment; you may not be shooting enemies on the other side of the globe, but you're still chasing happiness and distraction.
Happiness and distraction; that's what gaming is all about really and it's something that Minecraft, for all its abstractions and division, delivers in spades. You can build cathedrals with your friends; create macro-scale machines on your own or simply drift, floating through impossible landscapes that can bend to your will - do anything you want! That alone gives Minecraft a little bit of magic.