The problem 3.5e/d20 is that the system is founded on an incredibly forced class- and level-based core.
While this can be deemed reasonable to some extent for D&D in light of earlier version of the game, it is terrible for games like Star Wars RPG or, especially, Call of Cthulhu. I mean, they have EXPERIENCE LEVELS in CoC now for crying out loud!!! Anyone who ever played any of Chaosium's original versions of the game should realise in a few seconds just how utterly pointless that is!
And given that d20 revised D&D so severely that it was willing to kill off many of the "holy cows" of the past, it is inexcusable that the system is as rigid and inflexible as it is. A revision was necessary, yes - the old 2e system was horribly outdated. The problem with 3e is that it tries to fix all the things that didn't need fixing while holding onto all of those who were praying for revision. Classes are still heavily enforced, and the skill system is dictated far more than it ever was before. Sure, you can take whatever skill you want, but if you don't choose the "right ones" for your class and keep pumping them up, then your skills are utterly, utterly useless. That's what d20 is the worst system around - it tries to masquerade as an "open system of choices" when it's really anything but that.
There are far more elegant systems than d20 around. Indeed, I haven't seen a worse system made this millennium. I'll choose GURPS or WW's World of Darkness system over d20 any day of the week!