I take no credit for this solution. All credit goes to Dimrill. This is his guide from the xbox360 version of this game. I used this guide and it was very helpful. Thanks Dimrill!
According to other sources, the things required to reach 100% completion are:
Complete all 15 levels in Story and Free Play modes.
Complete all 11 hub missions in Story and Free Play modes.*
Achieve “True Believer” for all levels and hub missions.
Collect all 150 minikits.
Collect all 250 Gold Bricks.
Collect and purchase all 11 Deadpool bricks.
Save all 50 Stan Lee in Perils
Unlock and purchase all 153 characters in the game.
Unlock and purchase all 40 vehicles in the game.
*A note that I didn't "complete" the levels in free-play, just played through to get all the minikits and Stan and then exited and saved. So that means you only have to beat the entire level in Story mode.
If you're stuck at 249/250 gold bricks, you've most likely missed the brick for the flying race on the West side of the island. It's high up, almost on the same level as the Shield Heli-carrier, directly West of the central park lake, out in the surrounding ocean. (all directions assume that the X-men mansion is North, and the statue of Liberty is South)
Stuck at 98.8%? You've most likely done what I did and didn't realise that there are three separate vehicle spawn points. One for road which are at ground level, one for air which can be found on the rooftops, and one for water which is, erm, near water.
Stuck at 99.9%? You've probably not bought the one boat at the water vehicle spawn.