I suppose I didn't make it clear, but if I'm trading with note there it's CH I-no; I'm not talking about just kicking the note.
And while it hampers his mobility, it simply becomes a guessing game with note. If I can sj when I see note, normally it not only didn't hit me but I don't have to waste any meter to avoid it.
The hardest thing against I-no for Johnny is not getting air thrown all day. He's huge and slow and since Johnny seems to win most air v air in this match (air slash is good) you have to avoid being predictable.
I honestly don't see this match as any worse than 5.5-4.5 in I-no's favor.
As for your matches with A3, I'd have to go back and watch them but I think you're talking about big combos off CH 6p and stroke, right? If so, those are mistakes on Johnny's part; most anyone can get big, meterless damage if he catches the opponent in CH; I'm talking about offensive mixups and I-no really isn't scary without meter in that case. Dangerous? Sure, but who isn't in this game on offense?
Edit: A quick note about 2H. It can totally save JO in tricky situations, but the move is too risky and I know (from experience) that JO can start treating it like a panic button, which will get you killed. It's better to learn distancing for anti-airing with shit like 5p, 5k (it works), 6p and punch finer. Don't use 2H unless you KNOW it's going to hit or you have the meter to RC