I think Joker suffers from a problem that quite a few characters in this game suffer from. Joker as a character is not bad in his own right, he has a lot of really good tools, gun shot is nice and fast, he has a lot of safety and some decent overhead/low mixups, frame traps, jump ins, good down 1, down 2, down 3 and now a pretty good wakeup too. I think this is the same for other characters that are considered low tier. Swamp Thing is now a good character in his own right, Raiden as well and pretty much every "low tier" character has great tools when you look at them on their own.
The problem I feel comes from the fact that when you have a character in a game like Joker and a character like say Supergirl, even if Joker's toolset is solid (which I believe it is) there is no reason to play Joker over a character like Supergirl which is better and also has easier execution. Personally I feel this problem very strongly when I play Ivy. She can do all the same things as Supergirl she just doesn't do them as well and the execution requirements are quite a bit more than Supergirl's.
Essentially I feel like the problem isn't necessarily that Joker is bad, in fact I think he is really solid in his own right, it's just that other characters in this game give you a whole lot more for a whole lot less work. Characters like Supergirl, Superman, Black Adam, Catwoman all give huge rewards for very little execution and a very simple gameplan, where as characters like Joker, Ivy, Captain Cold, Raiden and Swamp Thing ask for a whole lot more in the execution, gameplan and matchup knowledge departments while only rewarding you as much as the more simple characters or not even as much.
So how would I fix the problem? I'm not really sure that you can honestly. I think regardless of how characters like Supergirl and Catwoman are balanced in the future their gameplan and simple playstyle will always remain, while Joker players will always be required to have their teeth combos on deck to reach the characters potential.
Maybe I'm just talking out of my ass but that's how I see it.