There are pros and cons for each style.
FO3 style pros include balancing weapon repair/damage to level, reason to increase repair early for better weapons. Cons are the added complexity and somewhat unintuitive gameplay that you have these items but can't repair them over a certain level 'because'.
FNV style pros, intuitive gameplay, repair things up to max if you have the items. Cons, loss of game balance due to low repair weapons, greatly decreased need of repair skill for non-crafting playthroughs means there's no real reason to focus on it at all.
It's worth pointing out that in each system your repair skill determines how well you repair one item with another. The greater your skill the more relative repair % you get from combining one gun into another.