Interesting to hear your thoughts @ArthurWynne.
I would agree with you that the game is generally well balanced, for example when I play as Grave I feel that I have a very decent change to win any matchup. However, like you, my experience has taught me that there are a small number of matchups (often involving Zane, Rook or Geiger imo) that could do with tweaking to move them from a pretty feelbad place to somewhere more reasonable.
Even if there is never a v3 of Yomi, I’d still want to figure out what balance changes would make the game better, as tweaking and analysing games is one of my favourite things to do. It’s a sign of affection, rather than a sign of something wrong with the game itself. I’ve modded a number of board games with house rules or fan rules because it adds to the enjoyment of those games. I’m totally up for doing the same for Yomi. I know it’s not everyone’s cup of tea, but I really love thinking about it.
I absolutely agree Troq just needs some small nerfs to bring him in line with the rest of the cast (small speed penalty to both J and AA imo) but I disagree pretty strongly about BBB and Zane needing a whole redesign, I think BBB can be problematic for some characters (poor sad boulder) but long range is imo a really interesting twist to the usual gameplay rather than a blight on the game. When I’m playing rook vs BBB though I’m not sure I’d say the same 
Zane is…Zane… but despite my frustration with him, I don’t think of shenanigans in quite as negative a light as you. I could forsee a less damage per card character with a similar ability not being an issue at all. For me it’s his resulting damage efficiency that’s irksome. Having that be so efficient *and* having a ridiculously safe big super *and* having 85HP *and* one of the best reversals in the game seems so far ahead of everyone else that I often scratch my head wondering how it shipped as is (probably the numbers, which aren’t as quite as bad as it feels when playing). So I’m for mild-moderate Zane nerfs to try and find something that means he doesn’t crush the majority of the cast straight away but also doesn’t lose extra horribly to our minorly nerfed Troq.
I don’t know what to suggest for Persephone as I don’t tend to play as her, or against her that much. I’m not sure she’s who I would consider the weakest character, as her vortex is real nasty and her hand denial is pretty brutal. I definitely feel like caution with making her better is quite important. Because of her nature, Perse as the strongest character could be really quite feelbadf for the game.
I actually have a barrel-load of suggestions for Jaina! I’ve played with her pretty extensively and feel like I have a firm grip on her strengths and shortcomings. Will post them up here at some point soon for you (and others) to read through.