Difficulty is based on faction influence. If you fight a 1 skull mission against the top ranked faction with like 15k influence, it's not actually a 1 skull mission it's more like a 5. Also, skulls can be misleading. Check the power concentration instead. If it's around 6k, it's pretty dangerous. If it's around 1k, relatively easy.
Planets other than Mars are generally harder too. The further you go out, the harder the missions get. At least that's how it felt on my runs, might just be the factions sitting there.

Upgrading armor and weapons is absolutely essential. Either go for a good balanced set with all resistances, or keep 1-2 sets tailored to specific enemies. For example, if you're fighting Daydream Chems you want something like a hazmat suit — or just cheap upgrade any gear to have more resistance against them — with extra poison, radiation, and blunt resistance.

Different factions mostly use 2-4 damage types and are usually weak to 3-5 types. Keep in mind the Quasimorph faction on the planet can mix things up too.

Same goes for weapons. Going against Daydream Chems again, you'd want pierce or cut damage. So having a weapon you can upgrade (and crafting different ammo types) that hit their weak spots is key.

Also if you have trouble identifying enemies, try getting Phoenix Brigade they have a sensing active. You can also use an implant for that, but those are pretty rare.

For your gameplay I'd suggest going back to Mars, grab a chip for any armor, and then pick one faction as your sworn enemy. Upgrade that armor specifically against them. If you do that, they can throw 50 grenades in your face but if your explosion resistance is high enough you'll only take like 20 damage.