The description is a little misleading, you need to MAX all of the skills, not just upgrade them.
You can upgrade either from your office, or hitting the start button and selecting "Stats and upgrades" while on a mission.
Then, hit the RB button and you can see the various unlocks and cost - you need to collect the yellow crystals to earn those unlock points by either:
1) Buying 100 from the gift shops ($1million starting price)
2) Receive 100 as a gift for getting a woman into bed (after all weapons unlocked through their gifts)
3) Kill enemies, some (especially stronger enemies) drop them.