I just think they should have done it from the beginning, while they were remaking the game, so ya now it's probably to late, and it's not likely that they will make such a big change; at least not before 4.0 expansion. But i have seen other F2P games, totally revamp the skill system, so it's not impossible.
I don't think skill trees is necessarily "complicated" you just put your points into the path of your choice - it's maybe just that to many options may be the downside - but at the same time it's less choices, cause you only need to choose 1 class/job, instead of 3 jobs (if you want to have 1/role) and instead of having gear sets (or also) you could have "tree sets" to quickly swap to another spec, just like you quickly swap to another job.
It would certainly be a lot of work to basically triple the nr of skills/builds, which in some cases may count as a new job, but it's basically the only option for adding new paths to old classes - with ACN you could get SCH/SMN, but that's because they built ACN with that in mind; they probably didn't have any plans for such a system, when they started out re-making the game.