There are puzzles like that linked to certain side missions like rescue all 5 riddler hostages (you need to gather 100 collectibles to get each one so 400 in all for all 5 sub missions) gives you 5 different inside locations to visit you would otherwise never ever see & some obstacles to overcome to rescue the actual hostage at each location using your gadgets (you may need to upgrade them all to complete some of these riddles though as they are impossible without certain upgrades).Sorry haven't explained that - the puzzles I really liked were the actual riddles:
You don't know Jack about Gotham. Tune in to find out.
You have to zoom in on the radio and scan the name on it.
Not the unusual perspective ones which were okay but not brilliant.
M.