Here's an nice guide I found about which pet to use when: When to Garuda Egi when to Ifrit Egi

As one of the comments put it - tldr go Garuda. On certain fights you may want to use Ifrit of course. Atomos is a kinda weird one where you might want to send Ifrit to attack but the bad thing is it's out of range of Spur and Enkindle. I also believe Garuda's contagion effectiveness was lowered due to Lightning being taken off cross class, but not enough to warrant switching. Unless min maxing though or in a dps race encounter, I just use Ifrit sometimes because I like how it looks and ruin spamming gets a little boring.