I feel anyone who can appreciate growth systems in games and was not raging over RME knew exactly that they needed some other method of character growth with the lv99 cap. Even I think going beyond it would be a bad idea.
The main issue with merits is that they're purposely lackluster with a handful of decent choices. I would rather job merits get entirely revamped and redesigned. Then and only then would I think it appropriate to give the jobs growth trees to further specialize or develop their jobs in a specific direction.Now I'm no developer, but would you consider a growth-tree like addition to merits? or a completely new system outside of merits. Something along the lines of spending growth points to climb along a growth tree, taking branches to get new traits or abilities, but make each tree job-specific, and make only one path available to be taken at each branch. That way you could have 2 drks, for example, but each would be unique based on the choices they made. Again, I'm no developer, and I'm sure there are holes in what I said, but it could be an interesting path to look into ^^