Unlock Breakthrough Nodes carefully, and afterwards make sure that you have some upgrades that are guaranteed (only money needed). By doing this, while you research those upgrades you will have more time to get the extra Research Points needed for future upgrades.
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Farm difficult Challenge missions for better rewards including money and Research Points.
When you see the option to scan an enemy appear above their head, capture that person by shooting down their weapon. Captured enemies are worth more points, however their monetary or Research Point rewards will not change.
Start by upgrading your pistols, then your costume. Save up for new weapons while earning free weapons such as the T2 pistol (by winning challenges).