How to gather resources to afford the later base upgrades

Staff Morale effects your soldiers abilities. When they are in good morale, they will perform better than their skills, indicated by a yellow boost to their bars:

The primary factor for Morale is GMP balance. Keeping a surplus is the best way to ensure that Morale is not negatively effected. You can also visit the soldiers individually at Mother Base to raise their morale.

Guide + Article

• Soldiers with high skills out in the field are rare. Without the scope the best way to determine an estimate of a soldiers skills is to consider their attire. Soldiers that wear high rank hats for example will have better skills than those who wear common hats. However, the scope is your key source of information on soldiers abilities and skills. Upgrade it as soon as possible, check what requirements you are missing, such as a lower than needed level in a particular ability branch of your Mother Base and do what you can to increase the level. Keep in mind that you also get volunteer soldiers after completing missions, so extracting is not the only means to get skilled soldiers.

• The population cap per division as well as the overall cap can be raised by building base structors for that division, building a command base structure raises all divisions population cap. Base structures cost resources and GMP, try to go through different interiors and side outposts in free roam to find the materials needed to upgrade your base.

• Fulton costs relatively low GMP to use in the field, try to store up on GMP when you know you will need it for Fulton (and resupply drops). You can build up GMP through doing missions, side ops, and operations with your soldiers. Other ways to gain GMP include extracting animals. Try to do missions sneaky and quickly for big GMP points (multiple hundred thousands), so long as you don't spend your points on upgrades that you don't need right away, you will have plenty of points to spare for Fultons. You can also increase your storage capacity and success rate by increasing your Support division in MotherBase.