I agree entirely with what Playtester stated. If there's really such big custom things in rAthena, why not work on the project itself to fix them and make them accurate?
(We're always looking for more skilled and dedicated developers, and the staff is a nice bunch of guys.)
This is the first time I heard of such a big issue, and the damage from official servers to rA seems pretty spot on to me.
At the end of the day, it's your decision and nobody can stop you from making and working on this new project, but we'd love if you could point out the flaws in rAthena so we can work on them ourselves at least. :]