First off, in the definition of roguelike (the only one that really works for both examples) is a game that requires repeated playthroughs (generally ending with death) in order to learn how to play it properly. This is the genre that made up the term 'losing in fun'. Also, binding of Isaac is ... kind of an arcade shooter roguelike with permanent powerups and other items. FTL is a pausable space sim roguelike where you control obtainable crew and weapons on an upgradable starship. Now, on to the introduction:
Somehow a debate on Twitter over Binding of Isaac came up, with JPH (@ninjagameden) complaining on Twitter (that's not how the debate started, BoI was a tangent) about it and other people trying to convince him "HEY it's not the worst game ever it's totally AWESOME!", eventually it came down to the point where JPH says that he HAS to use the wiki to know what everything does. Let's figure out how much of a problem that is.
Somewhat later, TimePyradox came in with some issues concerning FTL, and how it has specific builds needed to beat the boss that are specific enough to need wiki-ing. That's not really true (sorry), but FTL has other similar problems, and I'll discuss that below.
There's a lot of analysis here about these very specific problems, so this should be an interesting experiment. I'll have an answer as to which issue is the more serious one at the end. Now, one at a time, let's get into this. Binding of Isaac first.
Binding of Isaac
JPH's problem is he gets an item and he doesn't know what it does, and there's too many items for him to be able to learn through repeated plays, so you have to use the wiki during play to know what all the items does. I don't actually know if this is true or not - I'm sure some would agree, but twitter has accepted that he needs the wiki. (note, him specifically. This kind of thing depends on your capability of dedicating time to the game on a fairly consistent basis in order to learn the items well enough not to use a wiki)
He is arguing that FTL does not have this problem, because FTL tells you exactly what each item does, and here's the key part, BEFORE you get it. In Binding of Isaac, they don't tell them until after you get them at best, and never at worst. (Well, technically when you use it. That doesn't help when you get smashed by a giant foot because you're the only target)
In some ways, I think that labeling the items is irrelevant, because if it tells you after you get the item that's fine, as long as it tells you, because you pick up every item. The way Binding of Isaac supposedly works (I haven't played it) is that you take what you get, and develop a play style developed around what you get. Any combination of items (and you get a very specific number of items, usually, due to the way it's set up.) should be viable, as long as you know how to use that combination. Experience obviously helps with that, but it's not NECESSARY. You also get a pretty definite number of items, each of which benefits you in a supposedly equal way (although some are tradeoffs) Note tarot cards (a specific type of consumable item that do something when you use them) are an exception, but there's a relatively limited number (like 16? Less than 20 more than a dozen) Pills are ALSO an exception, but they have different effects every game, like potions in a classic roguelike, and typically won't hurt you directly in any way.
This issue (there are others that could be brought up, I'm sure, but this is the big one I've heard discussed) is relatively simple and easy to fix, so if that's the worst one, then Binding of Isaac is pretty well off in this comparison.
Pyradox's argument is that the builds required are specific enough that you need a wiki or spreadsheet to figure it out. If that was true, then that was bad. But I disagree that you DO. (He mentioned only experience players would when I mentioned this.) I've actually played FTL (I don't think I've written anything on it yet? I should fix that), and I asked Ranneko about this (Thanks Ranneko!), and as far as I can tell, this is just false. Specific builds that need memorization just don't exist. All sorts of tactics are close to equally useful, and you can beat the boss with all sorts of end builds. You DO need to be highly upgraded with full health, high quality weapons, a full crew, and things like that, but that's to be expected at a boss.
The problem, as far as I can tell, is that it's just a massive, MASSIVE difficulty hike from everything else. The rest of the game's difficulty curve as rough plateaus for each sector, increasing moderately whenever you go to a new sector, and then it just JUMPS at the boss. It's unreasonably difficult. It's so much harder new players will likely reach a skill level where they almost always reach the boss but never/rarely KILL the boss. (I'm pretty close to that level) This is an issue. JPH actually mentioned this in reference to Binding of Isaac, but the difficulty of a game (as an absolute, independent of progression. More on that in a second) should progress as a fairly steady incline, and rewards should roughly follow that. Character ability does the same thing in a progression based game, and the difference between those results in a 'perceived difficulty'.
The problem arises here: The absolute difficulty may increase by half again, or double. But the 'perceived' difficulty goes up by much, MUCH more. For comparison (this number is completely academic since there are no numbers involved), that value could be ten times as much as before (Note: as a difference, not a ratio. See post-post-script), the boss is that much harder. I don't think I need to tell you why that's a problem.
There are a few possible solutions, such as lowering the difficulty of the boss, and some other problems, like how it's the same every time (that's more subjective), but these are irrelevant. You can't fix this by something as simple as adding some text to the game, so I'd consider it a more 'fundamental' issue than the one discussed for Binding of Isaac.
Both games when played properly rely upon the experience of multiple plays to become proficient at them, so they do what they're supposed to as roguelikes. (note: FTL does almost exclusively, while Binding of Isaac also has twitch skill and other things that you need to play well. I'm discussing the roguelike mechanics specifically) I'm discussing two specific issues here, and considering they are some of the dominant reasons these games are NOT good (or fun, really. That's the hard part, distinguishing), I think that's a fair (but fundamentally flawed, it doesn't consider NUMBER of issues, just the single worst one) way of judging which is a better game. So qualifiers abound.
I'd say that the comparison of these two issues, which in Binding of Isaac is easily fixed and it's harder to do so for FTL, makes FTL an 'objectively' 'worse' game. This DOES NOT MEAN that it is less fun. It means that its systems are objectively WORSE. Any definition of 'fun' is inherently subjective, and just because a game is inherently 'worse' in this way doesn't mean that it's a problem. Although it is a problem. I would make the observation that they are LINKED, though. Actually, the idea that a game being 'good' is linked to it being 'fun' is pretty obvious, the issue is that when you ask if a game is 'good' you're ACTUALLY asking if it's 'fun'.
Note that JPH was completely unable to handle playing Binding of Isaac because of its obfuscation of mechanics due to a somewhat personal issue with not seeing information, while almost everyone who plays FTL notices how much harder the boss is, although only some people quit over it. For JPH, the game was less fun because of a certain issue he had with playing it, one roughly analogous to that of a colorblind person. (JPH: I'm not saying you're colorblind. Or even that your brain has something 'wrong' with it like a colorblind's person's eyes are. Brains are more complicated than eyes) The issues with the boss make FTL less fun for EVERYONE, making it... a worse game, objectively. So if you don't have the problem with not knowing what stuff does that JPH did in Binding of Isaac, and personal preference is irrelevant (unlikely), theoretically (THEORETICALLY) Binding of Isaac should be more 'fun'. Assuming 'fun' is dependent on a game's systems being consistent and following some kind of logical progression.
P.S. Don't forget to check out my post with my idea for an XCOM Propaganda series! It's the very last post :P Taking signups for soldiers and ideas!
P.P.S. *MATH NERD ALERT* Actually, what I called a 'difference' between the 'absolute difficulty' and isn't a difference at all, since you can't absolutely define difficulty. Well, I suppose you could, but it makes less sense that way. I'd call it a ratio. Absolute difficulty and character ability have the same unit (strength, basically. Like a Challenge Rating in D&D, applied to the PCs as well), and the ratio of those results in a difficulty, with 1 being, say, average. (You have to define 1 and average is good because it allows lower values and higher much more easily, making the whole system more flexible and easier to use) Note that a difference in that case would ALSO work, but is inferior for the same reason that facing 22 CR as a 20 CR party is harder than facing 10 CR as an 8 CR party. (or more drastically, a 3 CR enemy as a 1 CR party) Note the ratios: 1.1, 1.25, and 3.00. (It might not be that bad, because performance is randomly variable and CR doesn't necessarily follow a linear scale of ability)