Because certain lines are almost unbeatable except for with a few very specific variations. Although you can figure out those variations and Rune your own Heroes perfectly it means that getting defenses is almost impossible, and if you do run a defense that will defend against the SE meta then you get beat by something else too easily.
It also means that most of the fight pit and Coliseum lines will be similar which is boring and we can't use our other Heroes effectively in many situations.
It also means that you have to get into a starting energy and movement speed battle with your runes instead of being able to use more creativity with the other statistics that you could play with and theoretically make some cool variations For Your Heroes.
It also increases the likelihood that people can trigger animation freeze bugs to lock down the screen which is just annoying.
Probably more just off the top of my head.