I wish i could be more helpful in how to address this problem, but Miko is balanced pretty well. The only problem that i have found is that there are not enough Miko players actually healing teammates. They spend most of their time throwing kunai, because Miko does an INCREDIBLE amount of damage for a healer, only being surpassed by assassins, and not even all of them (Deande needs buff). My idea is to give him a Toxicity system (like Ambra gains heat or Galilea gains corruption) where the more he heals, the more damage he will do, so that Miko players have an incentive to both heal and attack. The idea is as follows:
First, reduce the damage on his kunai to a third or a fourth of what they do currently. Then, make the poison on his kunai not work by default, but instead, use some of his Toxicity to add the toxin damage to his kunai. He would gain Toxicity as a by-product of healing teammates, By his healing beam, his mushroom (ultimate), and mutations that heal. Basically, as he heals allies, he gains Toxicity (like Ambra gains heat or Galilea gains corruption) that then uses that Toxicity to add bonus toxin damage to his Kunai and Cloud of Spores, expending Toxicity. This system is already in the game and would be easy to implement, and would reward Miko players for transitioning between healing and attacking. Increase the accuracy of his kunai and adjust the gravity on the kunai (the arc) so that they can aimed easily in close range, semi-easily (a few shots to hit) in mid range, and pretty difficult in long range. Increase the Toxin damage to do the bulk of the damage, and make the toxin DoT unstackable, but able to stack the toxin from the kunai and the toxin from the Cloud of Spores. Add a mutation that allows one further toxin stack to be applied, maybe make it situational (if target is at full health, only on last shot before reload, etc.). You can replace a few boring mutations (one about reload speed, one about fire rate, and the one that makes his ult do damage) with more interesting mutations that involve his Toxicity, like making his ult generate 3-4x the Toxicity than it should, or making it so that when you heal someone and you are at max Toxicity, you use any excess Toxicity that you would generate to add some Toxin damage to the attacks of whoever you are healing. Make the timer on the toxin effect simply reset when attempting to apply it again. Then it will only let you do damage if you heal your teammates, and while the enemies are dying of toxin damage, you will benefit more from healing and regenerating your Toxicity than constantly attacking the enemy.
I think that this would make Miko a bit more interesting to play, and instead of being ONLY an attacker (as many people seem to be), or ONLY a healer, will reward people for doing both, and fit his character very well. Tell me what you think in the comments below, and for general Character Balancing, chek out my forum post on Hero Balancing and Changes.