Don't ask me why. I'm not sure. That's one of the first things I'm changing about my muds combat system. Saves and Armor class. I'm not sure why they need to be negative. It doesn't make logical sense to me.
A lower saving throw is better because in the old days your die roll had to be higher than the number. This lets you translate bonuses like +4 very easily: you roll x, which becomes x+4, which is good because it's further away from the threshold. You could of course reverse it and mutatis mutandis it would be the same thing.
Really, though, there's no terribly good reason for computer games to follow the exact same rules as pen-and-paper games with physically limited die sizes and all that. I think that a lot of things are the way they are because they are direct translations from a board-game RPG rule set (e.g. AD&D).
Some people really like a faithful adaption of pen&paper rules, I suppose because it makes it feel more like an online version of their favourite roleplaying game. I know I felt that way when playing D&D computer games long ago - I wanted them to follow the exact rules, to make it feel like D&D rather than a generic adventure game. I also created a WoD mud in the past, and that was pretty faithful to the rules (even going so far as to show the player the dice rolls).
However if you're not specifically trying to create a mud adaption of a tabletop roleplaying system, I agree that there are better approaches. Computers are great at the sort of number crunching that would bog down a pen&paper game, so you might as well take advantage of it.