I'm wondering how exactly weapons are going to fit into the development of your character when there's also a job system involved. Part of me thinks it might suggest different types of the same class (i.e., if you raise a red mage frequently wielding a sword, your melee capabilities may develop more than your magic) which would allow for some diversification within even the classes. While this would certainly be interesting, I can't imagine it would very much help the whole situation in FFXI which pigeon-holes players into cookie-cutter job combinations.
Then again, the perceived problem of cookie-cutter main/support job combinations in FFXI has never seemed as much of a problem to me as it has to other people. Some jobs are better paired than others simply due to their nature, and the ones that the community demands are the optimal, most efficient job pairings. People scream and shout, "I'm paying my money to play this game, I should be able to do what I want!" but I just shout back, "You're free to do what you want on your own time; but I'm paying too so don't drag me down if you want to play with an unorthodox (and frequently inferior) play-style."
Balancing between main jobs, on the other hand, is most certainly necessary, although I often think perceived imbalances between jobs are more frequently faults of the community as opposed to those of Square Enix. Certainly DRG was weak upon its introduction, but more often than not, such examples of weak jobs are usually just that the player base are, by and large, bad at playing said jobs. Case in point: puppet master. Take the average puppet master and they are, as the community loves to call them, a lolPUP. However, that's because the people playing them aren't willing to put the time, effort, and money into making a good PUP (all jobs take time and effort, and the economy in-game which drives the price of PUP gear up is controlled by us, not by SE). A good PUP can solo Diabolos Prime.
For those with attention deficiency disorders, here is a summarized snippet of the general ramblings for you to ponder over - the problem with job imbalance is as much the fault of the community as it is of Square Enix.