To obtain, The Number One achievement you must complete the game at least once, and gather all 45 flocks of crows within the storyline. Now you will have to continue onto another story mode to finish getting the last of the skills you need because one play through is just not enough. All in all, you can either repeat some missions to level up or just continue onto the next story mode.
IMPORTANT!!! --- When continuing onto another game be sure to chose "New Game +" or "Use last stats from a previous save file".
*** If you have already gotten all of the collectables and are wondering where you should look to see how close you are to the achievement go into the Options menu and select Statistics then you will see Skills Obtained XX/61. ***