The skills your champs use have damage-multipliers, that are hidden in game. You can look for these multipliers at some fan-made websites about the game, for example here.
Look at Athel, one of the starter champs. Her skill Divine Blades has a damage-multiplicator of 4,1 x atk.
Compare with Dark Athel (the undead version of Athel, given as login-reward at day 90). Most players think Dark Athel is a bad champ, and I agree. The real Athel is a much better champ than her undead version. Dark Athel's skill Blades of Blood has only a damage-multiplicator of 3,6 x atk. So even with a slightly higher atk she will do less damage.
/edit: Maybe I mentioned not the best example, as base-atk x damage multiplicator will see Dark Athel in front. But (real) Athel can buff herself before she attacks and therefore deal more damage. Doesn't matter at all, it was just an example to show the damage multiplicators.