The PRC implements weapon proficiency differently than the original NWN. A PC can equip any weapon, but at a -4 (I think) penalty if the character is not proficient with that weapon.
The balancing disadvantage is that a character can't take broad weapon proficiencies like "exotic" anymore. Unless the proficiency is part of your class, you have to take proficiency one weapon at a time, which chews up feats like crazy but is useful if you have found a particular uber weapon you want to wield.
To weigh in on some of your earlier questions, I'm not sure the advanced leadership feats are worth it, but I almost always take leadership, because having an extra pair of hands can sometimes prove quite handy. I think the NWN engine limits you to four party members regardless, so if you have two henchmen, a cohort, and a familiar, you won't be able to use summon spells. (At least this seems true in the modules I typically play, so I assume it is an NWN thing.)
THe custom cohort routine, alas, is still buggy the last time I checked. Standard cohort still gives you a fair amount of flexibility, but be aware that you can't summon cohorts from races added after 2.2c (when the leadership feat was lasts coded). They show up in the list of choices, but selecting one of them produces no result.
I think the crafting feats are worth it if you set the switch that allows arbitrary crafting. You are right that PNP crafting is probably only useful in a low magic environment. However, arbitrary crafting gives much more freedom to customize items. The feats that enhance crafting or lower costs won't work on arbitrary crafting, but it doesn't appear you need to take the epic crafting feats to craft higher level items; the regular feats seem to allow any level of crafting. The limitation is that higher levels of crafting are expensive in terms of money and experience, so the feats really only come into their own in situations in which you have a really good cash flow and can earn lots of experience. Otherwise, you won't be able to craft really high level items anyway. In any case, arbitrary crafting, as you can see, doesn't eat up that many feats. I find if I take "craft wondrous item" and "craft magical arms and armor" I'm pretty much set, and both are takeable by a fifth level caster, which means you can use crafting with a build that is not primarily a caster build. (Forge ring would be nice, but you need 12 caster levels to be eligible.)
To me arbitrary crafting makes more sense than PNP crafting. I encounter all kinds of weird magical items in mods. It makes roleplaying sense that someone must make them, but PNP crafting only gives you a few choices. Arbitrary lets you add any chracteristic in the toolset to any relevant item (again assuming you have the right gold and experience). This seems to offer a more logical explanation of where unique items in a mod could have come from in the first place. The cost factor effectively keeps a player from going wild and creating items inconsistent with the module. I can only get to really powerful items in really tough modules, at least those that reward victory well enough. And I like being able to customize to address specific menaces I find in a new mod. This adds a whole new dimension of planning (especially how to use resources, since both gold and experience are finite resources). Since the new crafting system was introduced, I generally try to create character builds that allow for crafting.
I recommend Endless Nights IV as a mod that enables you to earn enough resources to craft some pretty powerful stuff yet has a challenge level high enough to be tough even with some potent custom items. Also, you have to be pretty far along in the game (and thus facing a high level of menace) to really get into uber crafting. In other words, although arbitrary crafting gives you a wide range of options, the cost factor keeps the game balanced appropriately.
