Let's be honest, with the way he currently plays, if Johnny Cage had 50/50s that led into combos, he'd be utterly disgusting, as every single touch would end with you in a guessing game between high/low/grab, and in A-List especially, he'd be able to make himself safe every time you block correctly. Granted, there still are characters who can whiff punish with the best of 'em and still have 50/50s (Jax, for example), but I wouldn't say Cage needs them in order to compete. His f3 is a very good footsie tool and I would definitely say that its whiff punishing abilities allow him to play his game without the need for 50/50s, at least in A-List. On block, it grants him free pressure, and on hit, it easily leads into upwards of a 28% combo into restand, 40% if you can sneak in a grab at the end of it, all for no meter.
Of course, MUs where Johnny's f3 is outfootsied by other moves is where things get tricky, but the ability to backdash out of f3 on whiff can bait out a lot of advances, and those, you're free to punish. So yes, even if it isn't this amazing cover-all move, I do believe that his f3 makes up for the lack of 50/50s as it offers more versatility, and without it, he'd be nowhere near as good as he is now.
The guess between d4 and f2 is a 50/50 in the same vein as, say, the guess between Mileena's f234 and f23xEx-Roll. One option does piss damage, the other leads to a full combo, so it's obvious which one you'll want to block. And trust me, there are players out there who will NEVER block a d4 no matter how many times they eat it. And on the flipside, you have players who constantly block low after a d4 for some odd reason. d4 only counts as Johnny's only low combo starter because it jails into f3 on hit, but all your opponent needs to do is block and not try to press buttons like an idiot and they'll be fine.
The low damage from d4 doesn't make it an effective 50/50 tool, but it is a hell of a frustration tool. Again, it jails into f3 quite easily, so each hit basically grants you free pressure and meter build, and that's not even mentioning its low-profiling capabilities. Give it enough time and your opponent may start trying to block it. That's when f2 comes to say hello.
So even if it technically is a 50/50, it's a pretty weak one. The likes of Erron Black, Sonya, and Quan Chi see it and just laugh.
Unfortunately, I can't really answer this one that well as I've never played Injustice, but anyone calling 11(3)/11 (f2) a good mixup needs to play better opponents. It may have worked in the beginning when we didn't know any better, but Cage mains won't be getting away with that anymore. One armored interruption is all it'll take for them to never try that crap again. 1 (f2) is better, but a good player will quickly catch on to that one as well.