Merida played for both clubs earlier in his career.
He told AS: "I'd tell you it's 51-49% Atletico. I would give them as a favourite because I think they arrive in better shape. Anyone can win.
"I love them both. If Arsenal eliminates Atleti, it will hit me badly and vice versa."
On his former Arsenal manager Arsene Wenger, Merida added: "He has marked an era in English football, not only in Arsenal. The last years have been complicated, but what he has done is within reach of few. I was lucky to work with him and learn. He gave me my debut and I will never forget it."