The 49-year-old spent 18 months in charge at Emirates Stadium before being sacked in November 2019 and subsequently replaced by Mikel Arteta.
He guided Arsenal to the Europa League final and a fifth-place finish in the Premier League in what proved to be his only full season in charge.
Arsenal spent a club-record £72million to bring in Pepe from Lille ahead of 2019-20, but Emery felt the Gunners should have instead moved for fellow Ivory Coast international Zaha.
“I usually want to sign first the players I know,” he told Football.London. “When we played against Crystal Palace, Zaha showed he was a very good player.
“I also think Nicolas Pepe is a very good player. When you make the decision you have to decide how easy the adaption will be of some players.
“I was thinking the adaption was easier for Zaha because he was playing in the Premier League and you didn’t know exactly how fast Nicolas Pepe can adapt to the Premier League because I know you can need some time to adapt.
“I was thinking at this time that the adaption of Zaha was probably easier and faster than Pepe.”
📊 Most wins in their first 50 games with Arsenal…
32 – Unai Emery
28 – George Allison
27 – George Graham
27 – Herbert Chapman
25 – Jack Crayston
24- Tom Whittaker
24 – George Swindin
23 – Arsène Wenger
23 – Don Howe
— Arsenal (@Arsenal) April 18, 2019
Pepe has struggled in his year and a half with Arsenal, scoring and assisting a combined 13 goals in 42 Premier League appearances.
That compares to 17 goal involvements for Zaha across the same period in 11 more games, while the Palace winger also completes more dribbles per 90 minutes (3.68 compared to 2.92) and plays more passes into the final third (2.2 to 2).
Pepe’s inability to make an impact on games was one of the contributing factors in Emery’s exit and the Spaniard rued some of the decisions made during his second season in charge, though he reflects on his time in north London fondly.
“I was in Arsenal for a year and a half and first year I think was a very good season,” he said.
“We achieved the Europa League final, we were at the last moment with the possibility to be in the top four and I think last year when I was there we recovered a lot of confidence for the club and the fans and for the players and I think we finished well that season.
“I was very happy, enjoying it and working very well. The club supported me and I was happy with the players, the atmosphere and the supporters – only the second six months of the second year when I finished in November I think we made some decisions not good for the club, but not for me, the decisions of the club.
“When the results were a little bit bad the situation changed but my first year in Arsenal I remember a lot of positive things, on the sidelines the same. I enjoyed being a coach of Arsenal and I’m very grateful for that moment I had in Arsenal.
“For me it’s not negative, it was a positive experience and after I left the club the first month was not easy for me because I was running out of things [to do] but now I am very grateful to the owners, the club, the supporters, the players, the workers in Colney.
“I now only remember the very good things there and the first year for me was a very good performance for us.
“I worked well with Mr [Stan] Kroenke, Raul [Sanllehi], [Ivan] Gazidis during the first months there. The results towards the end were the main problem but for me it was a positive experience and I’m grateful to Arsenal for the opportunity.
“This is football. Now I want the best for Arsenal and Mikel Arteta, the supporters and everyone at the club.”
Another player Emery failed to get the most out of is Mesut Ozil, who has since been completely frozen out of the picture by Arteta and looks set to leave Arsenal this month.
Only Kevin De Bruyne (75), David Silva (63) and Christian Eriksen (62) have provided more Premier League assists than Ozil’s 54 since the start of 2013-14, but the German was regularly overlooked for selection.
Emery has defended his treatment of Ozil, however, by insisting he gave the playmaker all the guidance he could.
“I worked for one and a half years with Mesut and tried to help him, support him and achieve the performances for the team with him,” said Emery, who was appointed as Villarreal head coach last July.
“Now I don’t know what the problems are as I am very concentrated and focused with Villarreal. I follow every Arsenal match but I don’t know what the problems are with the team or the players.
“I can only speak about Mesut Ozil when I was with him there and I tried to achieve the best performances with him.”
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