1. Security: If the exchange offer 2FA or not and where the funds are stored. If it's not in cold storage, don't use it. If they get hacked, your funds are gone forever.
2. Reputation: This is based on the reviews you read about exchanges.
3. UI/UX: Not many people take this in consideration but I do. If there are multiple exchanges with the same security measures and reputation, I will take the most attractive one in UI terms and the one that give a better user experience.
I personally don't mind paying an extra fee If the exchange is worth it. I suggest using Binance, Bittrex, Hitbtc and staying away from exchanges like Yobit and Liqui.