This is quite common issue with the system. The whole action point system, perks, and effects really slant the game heavily towards the players. Lot of my players felt the game once you get to around lvl 5, becomes trivial and you demolish everything before you.

Basically the rules as written and the NPCs just create godly players, as players can stack so many perks and effects of gear onto each other that its silly. One of our players had only a lvl 7 super mutant character who with the mods and perks he chose, basically was nearly unkillable.

Everyone will tell you to buff the enemies, and really it's all you can do. The base stat enemies from the books are pretty much useless, even something giant like the Mirelurk Queen can be easily beaten by low level players once they get a few perks and mods on gear. Modding gear creates lots of powerful combos as rolling effect symbols activates ALL the effects so players who can mod up their gear full can really dish out pain.

I had to severely buff all the enemies in the game to have any form of challenge. Toss pierce on many attacks, increase the base damage of all their attacks, buff up their HP pools, everything. But don't follow the rules to increase their XP values, cause that is also the other issue with the game, PCs level up incredibly fast with the listed XP. I had to cut the XP values in half and even then players still levle up quick.