Pepe joined Arsenal from French outfit Lille for £72m last summer, but has struggled to make a lasting impression at the Emirates, contributing four goals and six assists in 23 Premier League appearances.
Alexandre Lacazette's goal gave Arteta's side a hard-fought 1-0 victory in the first leg, with Ivory Coast international Pepe only playing the final 15 minutes of the tie.
Speaking to Sky Sports News, pundit Charlie Nicholas believes that the 24-year-old should not start the second leg.
"I do not think this is a certain win for Arsenal. Mikel Arteta will sit and read into the fact that they let in two against Everton. Bernd Leno gets Arsenal out of a lot of holes but he did slip up for the second goal," Nicholas said.
"Joe Willock and Alexandre Lacazette will come in I think. You have to keep Pierre-Emerick Aubameyang in for his goals. Will Nicolas Pepe get another run? Probably. Does he deserve it? Probably not. I would probably look at Gabriel Martinelli."
Pepe contributed the assist for Aubameyang's winner in Arsenal's 3-2 victory over Everton at the weekend.