For Crash you must collect all 14 Golden Whumpa Fruits, use THIS GUIDE for locations, and you must also upgrade with mojo. The top left of your screen shows your upgrade bar, and mojo multiplier.
After the end boss fight against Cortex, considering you need upgrading, you can still wander the entire game and collect anything you might have missed, such as the Golden Fruit, dolls and mojo. If you need collect mojo to upgrade Crash or the mutants, first Get your Mojo Multiplier up to 20x by any means then head to the area leading to Mt. Grimly, SHOWN HERE. This will be you best bet for collecting mojo. So head to Mt.Grimy and enter in, immediately turn to the right and head right back out. Go along the narrow pathway, collecting mojo along the way, until you reach the steps going down to the right of the screen, then return back to Mt. Grimly. Simply rinse and repeat to collect mojo. Every time you enter/exit Mt. Grimly all mojo will respawn.
Whatever mutant you are on will be the one that's upgraded, if the mutant is in your pocket then you will upgrade Crash. The best thing is to jack two of the mutants you need to upgrade, so there is less running around to do.
Also, when upgrading Crash it's best to have a mutant to smash all breakable objects to release the mojo. Just make sure to have only one mutant so you can quickly swipe the breakable objects then pocket jump the mutant (), land and collect the mojo as Crash.