Are you using your weapon parts to upgrade your weapons? That’s one very important element in gaining the upper hand in a fight. Head to Viridia’s Shop in the Ark to upgrade them, and remember to attack scopes and weapon mods. Artifact Points are spent at Pripp’s Bar in the Ark.
You should sneak around and isolate single enemies and then attack them for as much damage as possible. If you have the three silent weapons (Crossbow, Ancient Pistol, MIMIR Needle Pistol) fully upgraded you should be able to take out singled out enemies with them. Singling out enemies and taking them out silently is a good way to gain a few extra levels. Even if enemies have a level or two on your characters, you should still be able to defeat them.
Finally, Bormin’s Hog Rush is considered a silent attack when you use it, and will knock out an enemy long enough for you to take them out with silent weapons.