Another problem with Fallout 3's stat system is that the Skills are very bland. Part of this is a very lacking participation from the SPECIAL stats, and another part is that tagging skills does nothing more than add 15 points to those skills. So for picking three "specialties", you don't get anything that you couldn't have gotten from gaining a few levels. It's boring, it's bland, and it makes you wonder why the game bothers you with it. Below, I'll list what could have been done when tagging any given skill to make the system seem more worthwhile.
Barter - 10% bonus to prices when buying/selling
Kinda boring, and still arguably useless, but lowering the amount of caps that can be found randomly about would make it more worthwhile to consider. Anytime you're running low on caps you'd be thinking to yourself, "If only I'd tagged that Barter." Another possibility would be modifying any Speech Challenge that involves talking about a price. After-all, your guy is supposed to be good at bartering prices, so why shouldn't he be good at convincing someone that he should pay you more caps to do a job?
Lockpick - Less stress on Bobbypins, and a 10% bigger "sweet spot"
So picking that lock becomes slightly easier, and your nimble fingers means that when putting torque on the lock in the wrong area, you aren't putting as much pressure on the Bobbypin, giving it about double the durability before it snaps.
Medicine - Added effect for most Aid Items
This would primarily effect chems, but also Rad-X, Rad Away, and of course Stimpacs. Tagging Medicine would of course be an option mostly for a player who plans on popping chems frequently. It would be a static addition per item, like +10% Health from Stimpacs and an extra 5 DR when using Med-X, rather than a blanketed percentile increase for all effected items.
Repair - More flexible repair options
Basically, this would enable the Repair ability that should have been there from the start. Without tagging Repair, it would work as-is where you need an exact dublicate to repair an item. When tagged though, you would have the ability to repair a gun using another gun that's of a similar class. You could tear apart a Laser Pistol to get a part needed for your Laser Rifle, and so forth.
Science - ?????
You know, I'll be honest. I'm completely stumped on how tagging could influence the Science skill. The only idea I can think of is going back to the bonus I proposed that Int could give to Science where it highlights options that would match the the chosen words.
Sneak - Enables silent running.
Simply put, it feels a little off that a stealth-based character needs to wait until Level 12 until he can do what his character is meant to do: Sneak. Even at 100 Sneak skill, your character will make too much noise and be easily detected unless he's moving too slow for it to matter that you're hidden. Thus, I'd propose to get rid of the Silent Running perk and simply make it the bonus for tagging Sneak.
Speech - Adds 10% success rate, and increases rewards for succeeding.
This one took me a while, and I'm not completely satisfied with it, but it's at least something. So when tagging Speech, it's easier to convince people you're right, and they'll give you more money for pointing it out. Say with Megaton, disarming the bomb rewards either 100 caps, or 500 if you win a Speech challenge, OR 600 caps if you win a Speech challenge with Speech tagged.
Weapons Skills - Adds 10% Damage when using weapons of that category, and...
Small/Energy Guns - Increases accuracy in VATS.
These two weapons types are similar in that they're great VATS weapons. Many of them have fairly low costs in VATS, so how else can they be improved but to make them a little more accurate? Something subtle enough that it isn't game-breaking to not have it, but noticeable enough that it can edge-out that low hit rate into something a little bit better. 10% sounds about good, makes that 75% chance to hit into about 82%. On top of the aforementioned damage increase with all weapon skills (and a few Perks that further increase accuracy), and you've got some good VATS damage coming.
Big Guns - Reduces the reload times by half.
The big problem with the big guns is that many of them are single-fire with a lengthy reload. A character who's going to focus on Big Guns though will be able to deal a lot more damage with his Missile Launcher than a character who didn't Tag the skill simply because he'll be able to put missiles into the air more frequently, with each one hitting slightly harder as well.
Melee/Unarmed - Enables a dashing attack that deals extra damage.
This one almost needs no explanation. As a melee-focused character, you'll want to close the gap with your opponent. Not to mention that the enemies already have these attacks, so it would have been easy to program-in the ability for the player to do them as well. To show when you can do the dash, perhaps an indicator would appear on your cross-hair. You would have to be far enough back that specifically backing-up to dash in would not increase your damage, but when dealing with enemies that are running away a lot, you'd be able to close the distance more easily with a hard hit.
Explosives - Allows for better throws when using Grenades.
I always did feel that Grenade-type weapons had a very short range in this game. Tagging Explosives would allow you to throw Grenades further, and at the same time would increase your accuracy in VATS when using them.