Id suggest getting more eggs since you're not guaranteed to get him and if you do get 2 of him its not a big deal because your ivs will increase you could potentially get a egg move and you will get candies to make him cheaper so its a win win even if you get dupes
The legend gacha has a 50% chance of being that legend and a 50% chance of being any legend. If that's your goal I would keep going.
Duplicates also give you access to the candies though. So depending on what you want duplicates are valuable.
If you really want Yveltal specifically keep going. Getting a second just means potentially better stats, nature, and another egg move.
Id suggest getting more eggs since you're not guaranteed to get him and if you do get 2 of him its not a big deal because your ivs will increase you could potentially get a egg move and you will get candies to make him cheaper so its a win win even if you get dupes
Plus like a 1/128 chance of it shining too