I do not think there is a problem with teh current skill/job system. Rather by taking esoteric's idea, you can expand on it and get a lot of ADDITIONAL features, without loosing any flexability. For instance, once you implement a certain job by combining the correct balance of skills, you unlock certain features, or maybe even start climbing a different tree of skills
For example:
lets say theres a class, thief
to become a thief, you must equip 20 action points of pug, and 10 of gld and once you do, you are a rank 1 thief. Perhaps you could do this from either direction, so you could be a blade wielding thief, or a punching thief. Perhaps tehre could be an initial pug guild pt cost to unlock it.
Now, as a thief rank 1, all new sp goes into thf, you can not rank up the source jobs without dropping the ratio (balancing this system also creates inherent limits, like you can not have a gld heavy pug without slipping into thf) as you gain ranks, you of course gain more points for attaching skills, and so you can use the thf specific ones this way, and of course you can go back to basic class and use some of the thf skills you've earned thus far.
you cuold always implement extended class specific weapons, so a dagger that is fragile/weak/lacking in special power unless you become thf after equiping it
it doesn't prevent you from adding new base classes, but it makes it very tricky (and not really practical untill leve cap increase) to make a 3rd tier of classes (so for instance, thf+samurai = ninja) which isn't really critical, sam+pug could be ninja too, and mighty fine at it given the list of pug skills...
also you could have another type of job, lets call it sub-job, made by specializing another one. So blm could be conj without healing skills equiped, and whm could be conj with no damaging skills equiped. Perhaps this capacity could be unlocked at the guild (buy blm subclass with guild points and when conditions are met, start ranking blm and gaining those spells, and perhaps a bonus, such as stronger bonus from your element attribute to relevant spells as long as you are blm)
this has the advantage of leaving a potentially lightly filled action bar to start eh subjob, whereas, as described above, extended jobs would have a relatively filled (unless you lower reqs) bar.