More popular? Pokemon, by far. Better? Fire Emblem, I'd say.
Pokemon is your typical kids' JRPG. Nowadays, it's mostly used as a brand name for Nintendo, especially when they want to make some cheap junk that wouldn't appeal to anybody otherwise - it's like an old slasher franchise where after the second or third film they'd stick Freddy or Jason in and call it a day.
Not that I can say much, since the last main game I played was Moon, but that seems to be the direction they're heading in, especially with spin-offs. Sword and Shield seem to be low-quality and I've heard plenty of complaints on how you could quite easily beat the game in under 20 hours, maybe even less than that.
Fire Emblem, however, has only improved objectively. Three Houses had some stunning feats of graphics and mechanics that I really wasn't expecting from my low expectations. I've been a fan of Fire Emblem for a while now and while the strategy has always been engaging and unique, Three Houses really blew me away.
Strategy. That's the main point here. Pokemon can quite easily be played if you keep going forward, using your strongest attacks, maybe grinding here and there. Fire Emblem has difficulty settings and can actually be quite challenging. In fact, it's designed to be challenging and have engaging stories, you could more or less do whatever you wanted with Pokemon and it'd still fit.