Pro tip :
#1 When taking a portal you will always find a proficiency item that will upgrade at the beginning of the level. For example, if you find the Biome 2 portal right at the beginning of your run and take it, you will find a proficiency item that brings you to weapon level 4, Biome 3 will bring you to level 9. Obviously you'll be lacking the Parasite, Artifact upgrades and you will need to find a new weapon.
#2 Leveling the different weapon skills are crucial. Many reason people feel that some guns are weaker is usually tied to the fact that they don't have any skills activate. Obviously some combination can be personally awful (I'm looking at you Charge Burst Pistol), while other combination can make you weapon you initially hated come very very strong. I initially hated the Electropylon, but after a few upgrade the dps was completely insane, same with full-auto on the rocket launcher.
#3 Always getting hit by the same skill? Some of those can be interrupted. The easiest one to explain are the flying Manta Ray (no clue what they are called in-game). When they glow yellow, it means they are about to do a melee attack which will more than likely hit you and do a lot of damage. Interrupt them with a few shots.
#4 Putting some time to do tip #2 greatly helps tip #1. With more skills unlock and their level 2 version (Havent seen lvl 3 yet), your gun will carry your through a higher biome with the lack of parasite and artifact. With will also allow you to do a complete run much faster.
Cheers everyone I hope some of these help!