no weapon upgrades this time, the upgrading for weapons is done in the lab room. you can both buy and find them and you can then apply the upgrades when you have enough minerals.
(you can never have enough platinum.... never) and as for ammo, as you probably saw with Jacob it is a personal ability. Also you can upgrade your armor slightly when you have the pieces in your captains quarters.
as for auto leveling.. like most bioware games they give you the option for your teammates. this can be toggled on and off... but be careful cause the computer does a bad job on a few characters, and unlike Shepard they cannot be changed after they go.