I noticed that, too. It almost seems like the game is set up to do the main story first, then after that's done do the side missions. The only problem is they're a huge source of experience points, and without doing/completing them your character might not be a high enough level to do well against the boss fights in the main story.
On a side note: I'm kicking myself for buying the Robin bundle. I thought he'd have a quest or two in the main game, like Catwoman does. Instead, it seems the only time you can use him is in those challenge maps that's outside the main game.
Nah you only need the gadgets that you get during the story,e everything else you get during level ups is just bonus.
And? He's quite fun in combat and predator.