Personally, I have always found a few of the restrictions sort of bizarre. A mace is basically an artificial club, so why can't a druid use one? Supposedly it's because of their "ethic," they can use a rough branch with a nail stuck in it, but not a polished wooden shaft with a metal ball on the end. But then in BGII they can use scimitars, and no other swords. That makes no sense to me at all. Why can they only use a sword if it has a certain shape? If they can use scimitars and daggers, it seems to me they should be able to use all swords. If they can use clubs, it seems to me they should be able to use maces and flails.
I think you shouldn't penalize weapon use too much. I don't see why a long sword should get in the way of picking a lock. Carrying around a big scabbard might reduce stealth and skills that rely at least in part upon stealth, like pick-pocketing and hide-in-shadows, but then where does the thief keep a katana, or are thieves like immortals in "Highlander," and have a magical disappearing scabbard in their coats? If a katana doesn't get in the way, neither should a long sword. A great big two-handed sword, though, would probably get in the way of everything. Also, consider that most thieves aren't that strong. With the exception of Yoshimo, most
NPC thieves are a bit weak. Considering that they are often the first ones to look inside a chest or tomb and carry out loot, I try to keep their loads as light as possible, and there is no way I would burden Imoen or Jan with a big heavy weapon.
As for mages, maybe instead of restricting the spells they can cast, you could increase the spell casting time. If a mage is wielding a bastard sword, he can still cast any spell he wants, but it will take him a moment to put the sword in its scabbard before he can start casting, doubling his casting time. The bigger the weapon, the longer it takes for him to put it away. In fact, the same could be true for all spell casters. I've always thought fighter/mages were a bit over powered.