EX Clones having armor would make Cage retarded, and pretty much unapproachable on wake up with meter, considering those options leave him + on block.
Most of what you named I really chalk up to match up inexperience, as most of his shenanigans can be armored through, especially 113 follow ups(A-List or Stunt Double). F24 being safe is nice, but it's -5 so it's not exactly like he's neutral and can continue pressure and also starts up in 15 frames, making it susceptible to a multitude of different pokes/counters. B121 in Fisticuffs also has a gap following the next 2, which most people don't even realize yet. Heck, most people don't even know you can back-dash the follow up uppercut from the EX Nutpunch for a full punish. People just take the hit.
I also said Johnny is probably high-mid, not garbage, so I do agree his footsies are good, but like I said compare these pros/cons to the other cast members. He's not blowing it out the water, a contender for top tier right now.