@infinita est lux Solis  
No, it wouldn’t. Making both sides OP doesn’t balance out the problem, it excaberates it. Consider this
 
is it normal for a single being to have all these powers or strengths in this universe?
 
What we consider here is…well we’ll use the three core pony tribes. It’s normal for earth ponies to be strong, it’s normal for Pegasi to fly, it’s normal for unicorns to cast spells. It’s not normal for any of them to be immortal. It’s not normal for an ascension to being an alicorn to occur.
 
If this is set in the Fallout equestria universe, remember nothing is immortal. Doesn’t matter what it is, it can be killed, and easily too. They piss off the wrong group, they don’t have game mechanics to save them. The way these three sound they’re just a case of,’ I can smite anything’. A swordsman, a pure mage, and a dark magic changeling are still gonna be gunned down.

@Background Pony #7773  
Well, what if their opponents are also overpowered, then it balances out…

I think I can tell you the main issue. Your characters are essentially OP immortals. In any universe, when the good guys are immortal and powerful from the get go, there is no tension. You already know they will overcome the challenges ahead as they aren’t really challenges