There's probably no clean fix while the weapons skills are divided, because the game needs item progression and investing in intermediate skills is so pricy. Really the only big improvement I can think of is offering a handful of quality, low-skill-requirement weapons like NV's Weathered 10mm to tide players over.
Still, the series has definitely advanced from the Temple of Trials approach, where it had been overdone to make the gameplay unpleasant.
First, perks (and to a degree points) felt scarce, especially with level caps. Dumping value into any combat other than Energy Weapons felt like you were backtracking when you switched over - though points were cheap if you took any of the meta-experience perks.
Second, that redundancy felt crappy because the energy weapons didn't really feel impactful enough. Some were fine, like the pistols, but the high-end stuff couldn't outpace guns. They were really heavy, and things like the Tribeam just weren't very good. The Gauss Rifle was solid, but you got it so late and it was so tiresome to maintain and keep loaded that it was hard to justify.
Really the biggest perks of Energy Weapons in NV were the low Strength requirements and the Hyperbreeder Alpha, which was a hilariously cheap and easy way to fight petty enemies. On some level the balance decision just felt wrong - I understand spending more to use Energy Weapons, but why would I if they don't beat Paciencia and Ratslayer?
In practice, with a build that maximized small arms from the get go (which also made the early-to-mid game easy), and invested stat points into Perception for those crits, by the end of the game you would be killing Enclave patrolmen with one-shot eye criticals more often than not, making any extra damage kinda moot.
(As I recall, gauss vs pulse is a long standing holy war in Fallout 2 community.)
It seems to me that the developers wanted to push players towards role playing a tribal who molds themselves to the wasteland. They wanted to discourage people from rolling a charming doctorate student with a Gatling laser.
I still think it's bad game design. It does make it less fun.