Atlas mechs are trivially easy to Charge/Nova to death. They fire discrete, powerful shots every couple of seconds; the odds that they happen to hit you with those attacks during your brief window of vulnerability are pretty low, even if you're not making any special effort to time your Novas to be invincible during their attacks.
If you double-Nova out in the open during a big fight where there are 5-10 enemies spread out beyond the range of a single Nova, shooting at you with automatic, rapid-fire weapons from all directions, double-Nova will not keep you alive for long. Using single, 50% strength Novas is almost guaranteed to keep you alive through every fight in the game except those where you face enemies in positions that you can't Charge to (barring situations like the bug where Charge won't work for a second or two, having a Banshee or occasionally even an Atlas do their one-shot instakill on you, etc).