The side missions can be fun if you like the way the game plays. I did. It's a tough game to 100% though because you need to also do all of the Riddlers revenge before getting true 100%.
I beat the game the first time then did all the side missions and Riddler's ? challenges. Then I tackled the Riddler's Revenge Maps, I really had to learn how to play the game for those Revenge Maps. I thought I knew how to fight and do stealth missions until I attempted the Riddler Maps, there was much to learn about how to really unlock all of the potential and use it in combat and take downs. Much.