The problem when you bring into the "realism" or "lore" argument is that the very idea of a 19 year old kid beating several armed security guards to death, escaping from the vault and then taking on an entire army of power armored soldiers single handedly is silly.
From a game play perspective, the "should energy weapons be rare" question runs into the same issue of the 10mm vs 9mm pistol change in TTW.
From a lore perspective, the pistol should be a 10mm one. But that would make the 9mm obsolete.
From a lore perspective, lets say you want energy weapons to be rare. So then you have players skipping several tiers and only using energy weapons in the late game when they have played long enough to get everything under the sun. And then nobody uses the low level energy weapons like the laser pistol, etc.
From a purely gameplay perspective, you could make energy weapon and ammo rare. Ok, but then whats stopping the player from spamming the wait button to get vendors to refresh? Pretty much nothing, so it does nothing except to inconvenience the player and encourage them to mod the game, while creating numerous balance problems.
As it is, i feel that guns are vastly superior to energy weapons in TTW, mostly due to the availability of things like HP rounds that shred enemies like albino radscorpions. Playing a guns character, by level 6 i had a sawed off shotgun, chinese assault rifle, lever action shotgun, .44 magnum revolver, 10mm pistol and hunting rifle. I was stuck with only a laser pistol for way longer than that in my energy playthrough. Plus the damage bonus from cowboy/grunt makes certain weapons much better than their energy counterparts.