If I play Captivating Poke Puff and find a Pokemon with the Omega Barrier Ancient Trait in my opponent's hand, can I choose that Pokemon to be benched or does Omega Barrier block the Captivating Poke Puff?
Yes, you can put that Pokemon onto the Bench. Ancient Traits are only active when that Pokemon is in play.
Source: TPCi Rules Team (2017-03-30)

Relevant cards

Note: All applicable cards may not be listed below.
XY11_99
XY5_151
XY5_24
XY5_60
XY5_77
XY5_86
XY5_9
XYP_XY49
XYP_XY49