Crocodile's secret is: He was a woman, changed by Ivankov.
Just for fun, this would open the possibility of him actually joining Luffy:
1. Ivankov knows something secret about Crocodile's past, something he is most embarrassed about!
2. There is no female "warrior" in the strawhat crew yet!
3. There is no Logia user in the strawhat crew yet!
1. Crocodile was originally a woman, and Ivankov used his ability to turn him into a man. Thats why Croco doesnt want anyone to know about his past!
2. Croco is a strong warrior
3. Croco is a logia user
Ivankov changes "Croco-boy" back to a woman and she joins Luffy & Co.
I dont think this is going to happen, like I said, it's just a fun idea. Imagine a fierce and arrogant female Crocodile joining Luffy, Usopp, SANJI and the gang
But about Croco being a woman, what do you think?