You can find Yveltal in a reddish orange portal with two glowing rings around it. Perhaps you could also find Yveltal in a more majestic (reddish orange) looking portal. Don't go in any portals that aren't the ones I described. It's also good to fly in the the Ultra Space for a while so rare portals appear (like one with Yveltal in it!). You may not get Yveltal on your first try. But you should eventually (like on your 2nd or 3rd try).
I hope this helps!
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