I like Minecraft but agree with some of his points. The crafting is fairly unintuitive and I remember Notch saying the same. The art is also shaky in places and again Notch did consider replacing it with the painterly pack, if I remember correctly. I'd also say a lot of the players agree that the base game has problems given how many like to use mods and texture packs.
I think that is a spurious argument. Any way you cut it, modding is going to increase the number of players of the game. The greater the breadth of mods, the greater the increase in players. However, I will say that modding is probably a good portion of the reason the Minecraft is so popular. There's only so much you can do with plugging blocks together, and while that sense of boyhood lego fantasy is what initially sparked so many purchases, mods are what keep the balance of players coming back to the game - whether because it gives more to do in single player, or because it offers rulesets for multiplayer interaction while maintaining vanilla flavor (e.g. survival PvP, N@W), or completely changes what the program is used for (e.g. an almost cinematic story telling experience).
Modding demonstrates how much farther Minecraft, as a vanilla game, could have gone on its own, if the Vision for the game wanted to go that far. I don't think Notch would have taken it that far, though, as demonstrated by the modest plans for the 'adventure' update which ostensibly culminated in The End. Maybe there is more depth planned, but it doesn't really matter, because we have modding after all. If Minecraft was not moddable, it would have probably peaked long before its official release, or occupied the same much smaller niche as its predecessors did.