I enjoy having a few things based on % simply for the reason that one can give increases or decreases in 1% increments, as opposed to 5% with the d20.
Seriously, tell something that happens in an RPG where having 1% granularity models reality better than the courser 5% granularity. Have you ever, for example, been about to throw a ball and think, if the wind were below 5mph it would increase my chances by 1%? Seriously? Remember every +1 or -3 in every RPG is arbitrary. Having less granularity makes it easier comprehend the difference. +4 x5 is 20% change, you can instinctively comprehend the gravitas of such a delta. +4 x1 is a 4% change. Compare 3% and 4%? Can you really feel
the difference in real life?
Naturally not, and it's possible that you wouldn't be able to notice a 5% change, either.
For example, in baseball scouts have a really hard time tellling the difference between a .260 hitter and a .320 hitter just by observation. Over the course of a major league season (say, 600 at-bats) the difference is one or two hits per week at the most. Random hot and cold streaks hide this difference to even the most astute observer.
My point is that we're trying to create a RPG system and the dice allow us to vary those numbers to whatever degree we want. If the GM rolls the dice behind the screen, the player would have zero idea if his character advanced by 5% per level, 4% per level, 3%, or whatever. As a designer, however, the ability to use non-5% improvements could be a nice advantage.
Maybe you want something to increase by 10% over a three level span. With a d20 you have +1, +1, +0 to allocate how you like, but that means that one level gets nothing. With percentage dice I could use +3%, +3%, +4% and make it more uniform.
Not sayin' DCC has to be done either way, just saying that percetage dice have a certain design perk. Personally, I prefer to roll d20's than d100's, but that's not the issue.