For one, unless you are a big body that 2-hitting move will whiff and be about as unsafe.
For second, you can armor through it as long as you aren't trying to do it as the move is coming out. As in as long as you are doing it somewhat meaty, it'll be stopped.
Third is it costs meter, if it manages to hit at all. MB lightning charge isn't a wake-up. Lightning charge is, and its not that hard to beat for a surprising amount of the cast.
Even Bane, which flash is his worst MU by far, has answers to it.
That's not to mention how useless it is when you corner the flash because you can mess with it for pretty much no cost on most of the cast.