I haven't played Mortal Kombat, but I'm subscribed to to Youtube channels for competitive fighting game videos - primarily for Marvel vs. Capcom 3 and Super Street Fighter IV, but I've checked out some Mortal Kombat videos. From what I have observed, and along with the commentary in the videos, the "counters" (or breakers, as they are more commonly referred to) and powered up attacks are not useless at all, and are actually more useful than the X-Rays. Many characters are capable of doing 30% to 50% combos with non-X-Ray juggle combos, making X-Rays a bit less useful, while making breakers a bit more useful so you can avoid this damage. Also, powered up moves aren't always just increased damage. They have special properties. For example, Kabal's powered up Flash cannot be stopped by projectiles, which is a huge difference. I think some others, like Reptile's run, allows him to get a combo instead of just a single hit.

