I have a few different suggestions which I'm sure will be hated. but here they go...
From what I've seen, it's generaly agreeded upon that clerics are overpowered in the NWN system. Nerfs on spells can be put in to place, (I dislike spell nerfs), or a focus on their alignment and diety can be taken into effect.
http://www.nwncityofarabel.com/coa3deites.htm Has a very good chart on dieties. In their server, they force an alignment of only 1 off from the diety, and the players must choose Domains that match up with the diety. This also offers a bit more roleplaying in the diety area, if people should choose to do it. The other thing they do is have certain spells adjust alignments. Example: Animate dead automaticly shifts the alignment of the caster 3 points towards evil if they arn't already evil. The downside of this system is that a cleric can fall from grace with their god, and a system has to be added in which they can return to their god, or profess their faith to another god (need DM help for that).
Someone else mentioned that Clerics should primarily be used with parties, yet parties seem to be hard to come by. My suggestion would be to put restricitons on resting... (thats the one I'm going to get yelled at for...) Hear me out though; the primary thing that makes clerics and even spellcasters very powerful is that they are able to slect their primary kill spells, use them, and then rest immediatly after the threat is killed. If people are forced to conserve their spells, they must choose when to cast their spells, and more importantly, they will have to take party members along to ease the spell casting requirements. There are several major downsides to this. The first one being, resting areas could become a prime place for PvP, means would have to be thought up and implimented to avoid this. (I have several ideas, but want to see how the initial sleep requirements go over before typing all of it.) The second, would be that other classes such as warriors will level easier, and quicker. It may even be advantagious for a warrior to avoid a party, since he then recieves more xp per kill. (Might add more synergy bonus or something like that.) The last problem, and one of the bigger problems, is that you would need to find a party member. Certain areas such as Gargoth have a low population, and finding party members could be very hard.
The pros to this system: Rogues would actually have people who wanted to party with them! (Ever tried starting out with a rogue? It's very hard to level.) Clerics would be more inclined to party with other people, and buff them, rather then get that extra offensive spell. Spell casters in general suddenly require more thought, and a certain extent of strategy must be used. In general, it becomes more worthwhile to party, leading to more player interaction for reasons other then PKing. It could also decrease the amount of PKing, as it takes more thought to hit a party with 3-4 members. (Or more planning and a few people with you.)
Overall, it would be a drastic shift to the server, I think it would be a welcome shift, but I'm sure plenty of mages are going to start screaming at me. So scream away, let's here what the thoughts are about this.