First it depends on your style of play.
Zombies are for Necromancer... Dark/Bad.
Atronach are more for traditional conjuror ... Good.
Now, zombies has a default: YOU NEED A CORPSE to make a zombie. And when the spell last, the corpse turns to ashes so cannot be raised again.
But it also has qualities: with Dead Thrall, you can choose WHATEVER NPC to be your dead Thrall, with his own set of skills. Atronach set of skills are pretty basic. Also, Dead Thrall don't turn to ashes so can be raised over and over again. So level 40 dead Thrall are usually stronger than the Atronach you can cast, but more specialized.
I would say that At the beginning of the game, Atronach are better. At the end game, Zombies like are better. But if you want to go that way, you will have to go and invest perks in BOTH branches of the tree.
Note: if you want a necromancer follower, Eola is great... if you get over her bad habit.