Alright, i'll throw out some ideas, hopefully some of them will be good:
The higher the rank invested the more money it cost.
Region bonuses: Extra cash earned, more XP in this region, merchant on mission field discounts, base vendor discount in this region, higher chances of a favorable find when investigating nodes (Finding loot instead of having to fight), discount on fuel merchants, fuel efficiency during travel (1 fuel reimbursed every/nodes), investing money to raise the value of missions in the region (better starting money and end mission payouts), etc.
Upgrades: Team mates cybernetic implants, weapons/armor one-time stat adding, more health to subs, more fuel capacity to subs, discount on rented sub prices, discount on mercenaries, discount on repair and refueling owned subs, more special missions available per informant payout, fuel start efficiency (Does not cost fuel units for # of nodes traveled ex: 3 first nodes cost 0 fuel, then fuel start degrading), etc.