Without her (or his. I don't know, why are ours characters so gender confused?) innate, many of his decent matchups would be 50/50 rather than 7/3 or 6/4. Amaya's moves are the "annoy the enemy to hell" type of moves. Shadow curse lowers the chance that everybody on the enemy team misses. Her (or his) shadow wrath chips away at all the enemies. Ninja port can be used to combo into Dark Chi Blast, or it can be used to stay away from close ranged enemies.
Any way you play her (maybe him), Amaya ends up being a very irritating character to play against with some ironicly good matchups.
Jade Figurine: Quite possibly the only ninja where this is one of the preferred items. Amaya loses certain matchups when he doesn't use this.
Scroll of Inner Focus: This item lets him ninja port 3 times before falling into the “no dark chi blast” range. Shadow curse goes down to 20 energy, so he can shadow curse over and over again without having to worry about having enough energy to use the move.
Flash Powder: As Amaya is one of the most fragile characters in the game, you may want to switch out more often. However, the Scroll of Inner Focus and Jade Figurine makes his matchups better. Use this if you want Amaya to be more of a hit and run character.
Note: I did do the math, but for a lot of these it’s too damn long to type out.
If it's tl;dr for you, skip to the end for a summary.
vs Cornelius: This is one of the most hilarious matchups, as Amaya happens to be one of the few good characters against corn. Corn will most likely not get a pilebunker off due to ninja port and amaya’s innate. It takes 4 voidstreams in a row to kill Amaya, but unfortunately for Cornelius, there’s a 60% chance of one of those voidstreams failing because of Amaya’s innate. If Amaya equips a Jade Figurine, it takes 5 voidstreams to kill Amaya with a 70% chance of one of those voidstreams to be unavaliable. Even if a voidstream fails, Cornelius has to face a Dark Chi Blast. (thanks to northern for helping me out on this one).
vs Tafari: On average, it takes Tafari 4 poison darts to kill amaya (including procs, I haven’t done the math for without procs) (also for both jade amaya and scroll amaya). However, like before, there’s a ~60% chance that one of these is gonna fail if you do them in a row, and that’s not counting miss rate. Starting at close, Amaya’s moves would be ninja-port -> dark chi blast -> rest -> dark chi blast. However, Tafari can close in, which would mean Amaya would have to ninja port again. This means that Amaya’s Dark Chi Blast has to proc in order for him to win. Of course, then there’s the chance that Tafari’s poison dart gets disabled. I’m guessing this matchup is around 5-5 or 6-4.
I have not done the math if Amaya uses Shadow Curse, however. If anybody else would like to do it, go right ahead.
vs Marquis: It takes Marquis 2 Vamp Touches to kill Amaya. He can get the first one off (~75% chance), but definitely not the second one. (apologies northern, your math was wrong :P). If amaya ninja ports as his first move, Marquis can’t get the second one off. After a VT then a teleport, Marquis is left with 45 energy, which isn’t enough for another VT. However, it takes amaya either 2 ninja ports and 1 dark chi blast + proc, or 3 ninja ports and 1 plain dark chi blast to win this matchup. I’m guessing amaya has a 9-1 advantage here.
vs Juju (thanks to CMiner):
Amaya has a huge advantage because his Ninja Port is speed 5, which lets him avoid all of Juju’s close range attacks, provided he has enough energy. This puts the fight at far range.
Hex only does 10 damage to Amaya, but will kill him in 6 hits (7 with Jade Figurine). Amaya’s innate should disable Hex at least once in that lineup, giving you at least 7 turns to take Juju out.
The real danger is Healing Touch, which can prolong the fight and drain your energy. This is why you really need Scroll of Inner Focus for this matchup.
Starting at close range:
Ninja Port -> Chi Blast -> Rest -> Chi Blast -> Rest -> Chi Blast -> Rest -> Chi Blast
If Juju does Healing Touch every turn, without Burn procs or disables on the healing touch, he will be at 20 energy and 5 health by now, and you with 25 energy, enough for another Rest -> Chi Blast. But most likely a proc/move disable will let you win this fight quicker than with 5 Chi Blasts.
The worst Juju can do damage-wise is 20 (2 hexes at far range). The biggest issue is how much energy he can drain from you before you kill him, but with a 25% chance of disabling Healing Touch each round, and no chance of an up close attack, this should be an easy, if long, matchup.
Basically, Amaya can win against some of the more powerful characters. However, this section assumes that it's the last two characters, full energy and full HP at close. It also assumes certain items. If it's not the last two characters on each side, Amaya has to worry about intercepts, and it's pretty likely that he'll get destroyed if an enemy switches out to a fresh character.
When Amaya uses Shadow Curse once, there’s an overall 40% chance that a move will either A) be affected by Amaya’s innate or B) Affected by shadow curse and will miss.