To all you who say they shouldn't have combined throwing and traps: They didn't. Explosives only helps on explosive traps, the rest are covered by repair (such as the combat shotgun trap.) What they did was take the portion of traps that applied to setting timers on bombs (really, I need a skill for that???) and added the ability to throw grenades. Grenade throwing IS actually very, very different from knife, shuriken or spear throwing. Before an experienced soldier throws a grenade, he/she can "cook" it by holding on after pulling the pin - thus giving the enemy less time to run away or to throw the grenade away. This is actually what your character does in Fallout 3 - a well-thrown grenade by a highly skilled character will explode the second it hits the ground by an enemy. A poorly-thrown grenade will land and give the enemies time to say "Oh crap" and run away, reducing or eliminating the damage (yep, this really happens in-game). So yeah, I think they did right by creating an "explosives" skill and getting rid of the nonsensical "traps" skill. As far as the Throwing skill, I think it makes sense to get away from that as well. How often have shurikens or throwing knives been used in actual warfare IRL? Very, very rarely. And Shurikens don't really fit with the fallout setting anyway. Thrown spears have been used for ages for hunting (and the Romans used pilons for warfare)), but they weren't all that fun in Fallout 2, and it's pretty unrealistic for your character to be carrying more than a couple.
I think they did a great job determining what skills to keep and what to get rid of (especially compared to the Van Buren decision to combine energy weapons/big guns/small guns - WHAT??). I wish they had allowed advancement over 100, though - that would have been fun. I also wish they had kept Outdoorsmanship and something a bit more similar to the Fallout fast travel system.
I think the biggest thing that they did right, though, was an escape from some of the Fallout 2 silliness - the "let's make the player a pornstar!!!! even though no one owns a television anymore and there are no movie theaters" stuff. Fallout 3 does a great job of showing the 50's culture and the real roots of Fallout.