I see your point that Joker has options in both MU's. However, by no means does that outweigh the hefty advantages both Bane and Fate have over Joker.
Before I start, I wanted to point out that you're explanations make it seem as if you're not thinking about both characters playing at the highest level. For example, a good Bane will never full screen charge. And a good Fate wouldn't just spam mindlessly. And you take into an account that Fate players "simply doesn't know what a combo is." Points like these aren't valid to dictate a MU number. Nevertheless, I'll do my best to go in-depth on both MU's.
Bane: It really does not require that much patience for a Bane to get in. Yes, he shouldn't do full screen charge, cause that means we get a free combo, but a good Bane who actually knows the MU would never do that. Instead, he will duck gunshots and get a dash in to (very effectively) close the distance between the two. Once he gets in, it's hell for Joker. With his normals, armor, and specials combined, I'm sure Bane is effective against many characters, but it's even worse for Joker. As I have already addressed before in multiple threads, Joker's neutral is garbage. Bane's D1, D2, and Command throw shuts down Joker at footsie range. Once he gets the knockdown, it's very hard for Joker to get out because he has no wakeup. So we mostly rely on delayed wakeup or a lucky backdash. I find that delayed wakeup is also pretty useless because, after, let's say a command throw knockdown, Bane can do another command throw, D1, or D2. These all have good enough recovery so that, when Bane recognizes that Joker is doing delayed wakeup, he can still go for another mixup.
In summary: It's really not that difficult to get in as long as you don't rely on charges (so the whole teeth combo thing is pretty null if you actually have a good opponent). Bane footsies > Joker footsies. Only thing I'd say Bane would have to respect in neutral is our teeth throwing. Not going to downplay and say it's easy to avoid, but Bane has enough mobility and range in footsies to deal with some teeth throws. On knockdown, Bane destroys Joker. There's no way in the world that Joker's "zoning" makes up for the massive amounts of damage Bane can afflict on Joker knowing that he doesn't have a wakeup.
Fate: Joker DEFINITELY does not outright beat Fate in zoning. However, Joker can somewhat compete in the zoning war in hopes of getting closer (because he does not win zoning). A good Fate would not mindlessly spam. He will respect our gunshot and be patient for MB gunshot. From there, he has fireballs, orb, or aux to effectively keep out Joker. All of these tools favor Fate, and the uses of these tools will ultimately prove more effective than Joker's zoning tool, gun. Even when Joker does make his way in, Fate's F2 is super effective in footsies because Joker has nothing to compete with that. If Joker gets a combo in, it's not like it's super easy to just keep doing setup after setup either because Fate has a wakeup that puts us back at a far range. Granted, there are ways around it, but it's still a solid option if you combine that with delayed wakeup (which destroys all of Joker's setups).
Hope this helps depict the MU realistically in high-level gameplay. Comment again if you'd like to disagree or argue my points or just want some help in a MU
