Bethesda's attempts to remedy it have involved buffing up their enemies in terms of damage and health, which still doesn't make the game more challenging; it just made combat tedious and the world make even less sense than before. All difficulty problems lie solely with the player's many powers, and the only way to truly make the game challengiing is to nerf them. There's no reason that the main character has to be far stronger than the NPC's statistic-wise in order for the game to be playable. Typically, the fact that the protagonist is driven by human intelligence rather than AI is enough of an advantage over the computerized opponents.
You can toss out eating/drinking systems because that wouldn't be fun in a game (and rather boring and tedious). You can toss out the need to use the bathroom regularly, to need to get sleep, and the need to spend years training to wield those weapons without killing yourself. You can explain away the fact that your character is a decent fighter instead of a weak, sheltered young advlt because combat wouldn't be fun playing the latter. But the fact that you are practically as strong as a Brotherhood of Steel paladin almost straight out of the Vault (and is capable of easily beating one too)? There ARE lines that can be crossed in regards to the "it's a game" rationale, and Fallout 3 definitely crosses them.
The LW's super-human status makes no sense from both story and gameplay perspectives. Had he/she been on par with most wasteland NPC's, it would've IMO been acceptable as far as the realism/entertainment balance goes and yet gameplay more enjoyable.