I'm really not a fan of either, but Nendos are substantially better than pops, by far.
Price-wise, Nendos are more expensive, but you get option parts a generally higher quality product; whereas pops are cheap because they're designed to sucker people into impulse buying multiple figures. It's quality vs. quantity.
Nendos also manage to capture character likenesses fairly decently despite the stylistization and you can even end up with characters like Kirby, Arale and Poptepipic whose designs aren't compromised too terribly and even work well; whereas pops force their aesthetic onto everything to the point where they manage to ruin fairly simple character designs like Pac-Man by making him square, but will sometimes be inconsistent and make a figure that barely looks reminiscent of the pop styling.
My only real gripe with Nendos is fairly negligible, and it's moreso that Goodsmile will get the rights to something and often end up making a Nendo instead of a figma, which sometimes results in a property being split up like figma Snake and Nendo Raiden, or Zelda figs being split 50/50 and resulting in janky displays.
My gripe with pops is they're literally everywhere I go; occupying way more space than they ought to be, attracting the worst kind of normie shitters that brag about their crap collection of a million in-box pops, and just generally being lazy, uncreative trash.
As much as nendos don't tickle my fancy, I could only hope funko goes bankrupt so I never have to see another one of those dead-eyed hunks of plastic dogshit again.