I generally don't tag weapon skills, going instead for support skills such as Repair, Science and Medicine. During the early part of the game I'll put spare skill points into Small Guns, and generally I'll still be at Small Guns 100 before the Enclave turn up. Once the Enclave turn up, of course, my spare skill points go into Energy Weapons.
So - early game, Small Guns. Late game, Energy Weapons.
So - early game, Small Guns. Late game, Energy Weapons.