the ending you got isnt "the bad ending" its THE ending. I'm having a dandy of a time with one of the "augmented reality training" points, the one in the bay off of one of the cranes. I cant seem to hit the 3rd ring no matter what. I have about 100 riddler trophies, but I honestly dont really feel like going on a scavenger hunt. The tragic part is the "side story" section in the upgrade menu, is practically empty, and I have no clue how to find them
There are a couple of other endings, though not the "true" end.

If I remember correctly, for that one you have to do a slight dive bomb then pull up. I found the first 4 to be really easy though.
The incentive to do the riddler trophies is that for every so many you collect, you get to face one of the riddler's death traps and rescue a hostage. Collecting them is the only way to progress the riddler side-story. That being said, there's a lot more variety in this game. At least half of the trophy puzzles are really clever, and at least for me they are fun to figure out. You do know that if you interrogate "green guys" that they fill in your map with locations right?
Let's see... side stories.
One involves finding Nora. The location is basically marked on the map.
Another involves finding Mr. freeze's missing gear, it's in the steel mill just like Harely blabs when you find her gagged up.
One is saving political prisoners from getting beaten up, they show up as blinking hexagons on your map randomly... after you've saved so many you are done.
The sniper case involves checking victims for clues... as you get more data you'll be given more locations to check. (I think they might unlock as you get in the vicinity of a body).
Phone call killer is self-explanitory... answer ringing phones and do what they say.
I haven't figured out how to progress the indentity thief yet.
The watchers are just red guys watching you from odd, out of the way areas. (They are usually up really high) when you find one talk to them. After 4 you are done.
That should get you started.
