I think the real problem with this is evidenced by Fallout 2's sloppy design. In Fallout, you could start with a 10mm pistol if you were a small gunner, but in Fallout 2, you had to go through quite a bit just to get a pipe rifle, and like you said, god help you if you want to tag Big Guns or Energy Weapons.In every single fallout game, you really only have the choice of picking Small guns, Unarmed, or Melee at the beginning. If you were to take none of those, and tag, Big or NRG, you would have a VERY tough time getting to the point in the game where you could actually use those skills.
The obvious solution is to provide some low level weapons for each category early in the game. The only thing that needs to be addressed is world continuity, as I can imagine it would be hard to justify an energy wepon of any kind in the predominantly low tech starting locales in previous Fallouts.
But thinking about it more, what if Big Guns and Energy Weapons are intended as "extended" or supplementary combat skills? It's obvious to some extent that both are high end weapon skills, but I don't think it's entirely fair to a player who chooses to NOT tag Small Guns to have to compensate for the lack of suitable weapons early in the game. Not to mention that having skills intended as supplementaries clashes with the whole philosophy of an open ended system.
Which brings us back simply making the choice of Big Guns or Energy Weapons more valid during the early stages of the game.