I think I agree that EC seemed to have at least put a really optimistic spin on what seem to be more design flaws than anything else. But I do see where they're coming from. (Disclaimer: I know approximately zero things about Dark Souls II.) I think I agree with basically everything they say at the beginning, talking about why letting the player choose an explicit difficulty level is bad, why offering help can be bad (I always get offended in the newer Nintendo platformers when they offer help after you die a certain number of times), and why giving you an option to switch difficulty in the middle of a game is bad (I think they even understate this point; I feel like much of the point of playing a really difficult game is to be able to say you did it, but if I'm constantly switching difficulty throughout the game, there's no record of my having done the hard parts (though I guess some games fix this by keeping track of which levels you did on which difficulties or level-specific collectibles/achievements, etc.)).
So, I guess what their point is is that DS2 avoids all of these issues by making a much more implicit "difficulty setting" system. You don't go choose "easy mode" or "hard mode", you play with weapons or whatever that make it easier or harder. And I can understand why this is better than an explicit difficulty setting, but I do agree that EC seems to overstate it. I imagine it's somewhat similar to maining a low-tier character in Smash Bros. In theory if your goal is to win, you should really just play MetaKnight (or Pikachu or whoever's top tier in Melee or Smash 4). But there's a certain satisfaction you get from being able to say, yeah I play Yoshi even though he sucks, I play him because he's an adorable green dino and how can you not love that. And I think EC is saying it's that same sort of feeling when you play with a "bad" weapon in DS2, you feel like, yeah I know weapon X is bad, but I just like it because it's fun. And then they're saying, most people will find themselves more attached to suboptimal weapons, but if they need the game to be easier, they can just switch to the "better" weapons, and they don't feel like they're cheating or doing anything they're not supposed to.
So I do see their perspective, but I have trouble agreeing with it. No one says it's a good thing in Smash Bros. that there are bad characters and good characters just because it gives you that sense of satisfaction when you win with a bad character. Everyone would surely rather have it be as balanced as possible. And same goes for FE, EC complains about lack of balance in FE (I think, I don't really remember that episode), rather than praising it for giving you an implicit "easy" or "hard" mode. However, I think there are good reasons to say that a game like DS2 is very different from Smash Bros. or FE in a way that makes EC's perspective on this more plausible. First, DS2 is (I think?) a single-player game (or at least non-competitive). So unlike Smash Bros., you don't feel like you're disadvantaging yourself by playing a bad character. You just feel like you're setting yourself up to try something new, and maybe more challenging. And second, I think (again I'm talking about a game I know nothing about) DS2 is a more action-based game, in contrast with something like FE. In FE, the game is all about making the decisions that maximize your chances of winning, so if you give players options that are better than other options, well, they should just pick the better options. If they didn't do that, they wouldn't really be playing the game, since the whole point of the game is to pick the right options. Whereas in an action-based game, the choices like that are presumably not really the main point, they're there to give you diversity, both in playstyle and in difficulty level.
Anyway, I really like Extra Credits normally so I probably have an irrational instinct to defend them. I think at the very least they really overstate the "genius" of Dark Souls II in this regard though. But there is probably something to be learned from it; I think it's good for game designers to be thinking about alternate ways to go about difficulty options, and the way DS2 does it is probably better than most games, just not by as much as EC is stating it in this episode.