Ash has given some great advice, but I disagree with just a few of his points:
1. Animal Friend works against molerats, brahmin, dogs, and yao guai. Among these, only yao guai pose anything close to an actual threat, and they're relatively rare. Additionally, since yao guai can only attack with melee, you can kill them fairly easily if you backpedal while firing at them. Therefore, I have never found it worthwhile to put a perk point in Animal Friend, much less two.
2. There are quite a few great energy weapons outside of the Mothership Zeta alien weapons. Most notably, there's a unique plasma rifle you can obtain in Rivet City that pretty much owns everything in sight. The Pitt has a laser shotgun that's also excellent, while Operation Anchorage gives you an energy-based sniper rifle.
Now, regarding your intention to build your own weapons, I regret to inform you that Fallout 3 isn't a great game for that. There are only a handful of craftable weapons, and before you can craft them you need to find the schematics for them, which isn't always a trivial task. Admittedly, many of the craftable weapons are considered top of their class (eg the Deathclaw Gauntlet is probably the best unarmed weapon, the Bottlecap Mine is the most powerful mine, the Nuka Grenade is the most powerful grenade, etc), but specializing in craftable weapons will be quite challenging for a first playthrough. Also, there are no craftable armors.
For your first playthrough, I heartily suggest a stealthy sniper playstyle, with a focus on the Small Guns skill. A stealthy approach helps you assess a battle before you engage the enemy, while sniping from afar gives you the chance to take down enemies before they even get close. However, do bear in mind that the sniping mechanics in FO3 are quite broken, so a sniper playthrough can cause a bit of raging. (I can elaborate on this point if you want)
Remember to save regularly, in multiple slots. FO3 isn't a very stable game, and there are still quite a few annoying bugs, some of them easily game-breaking.
Finally, let me re-emphasize what has already been said a few times: Explore, wander, do sidequests, soak up the atmosphere. The main quest in FO3 only accounts for, I'd say, 10% of the game. The true meat of the game comes from exploring the world Bethesda managed to build.
Oh, and after you've played through the game at least once, you can get into mods. Glorious, glorious mods.