So assuming Final Fantasy XV does release in 2016, will Pokemon eat its lunch, or will the separate ecosystem keep it safe?
If it honestly releases in November as slated... yes Pokemon will eat into it. I don't know if it will "eat its lunch" to the limits of that proverb but it will certainly impact part of its buying populace. Both are premiere jRPGs with one being considerably more "premiere" than the the other nowadays, and Pokemon has been resoundingly positive with its changes and current on-goings.
But how much it will eat into it is a different matter. It could be very minor, to the point of irrelevancy, or it could be noticeable. Used market being strong and FFXV being single-player means there's no real rush if you are otherwise engaged in a different product. And the I'd wager that most everyone who owns a PS4 probably owns a 3DS if they are j/RPG fans.