Before you could upgrade your weapons to take on missions with you, but now you can't choose what to bring with you. So what is the point of upgrading the weapons? And also what can you do with the money as it doesn't really do anything in single player.
There's no choices on loadout or weapon upgrades. The only "updgrades" you get are via gameplay challenges and they're skill based and applied automatically as shown in the grey boxes that pop up in the menu at the end of a level.
You can find a list of challenges almost anywhere, but I've yet to find a guide that details what rewards are given for each challenge, so skill rewards might be given for the number rather than type of challenges completed in each level.