I see absolutly nothing wrong with having a big guns and small guns skill. The "problem" that Fallout has, was that big guns couldn't be aquired early in the game, which means that this skill is pointless only in the beginning. There are more ways to "fix" this issue instead of merging skills. One being that you can introduce low-tier big guns, which the player can find and use even in the beginning of the game. The same is valid for energy weapons.