While I'll agree some of the weapons are just pure crap (measures and handbombs, wtf?), the balance in the game weapons-wise is pretty good. The statistical reason you want to limit what weapons you have for characters is that it costs license points for everyone to learn a certain weapon. If I just ignore a large part of the weapons grid and focus a character on particular weapons, it gives me tons more license points to spend on augmentations and accessories.

Additionally, it lets you be able to use accesories and armor that are most effective with your selected weapon. For instance, the genji gloves work great on any character, but if you put them with a katana/pole user, they become a comboing machine. Also the bubble belt with a tank character makes them nearly unstoppable and no mage is complete without a cat-ear hood or sage's ring..