Uhm. This isn't exactly in line with the current flow of this topic, but in terms of challenges for spellcasters, I do have a few ideas. I've got two hefty spellcaster PCs left in my surviving retinue of characters, and I think I could give a few ideas...
One almost universally unused aspect for spellcasters is counterspelling. I have VERY rarely seen a PC caster in NWNs devote themselves to countering magic. The system has flaws, mainly. The caster can only attempt to counter a single target, focusing everything on it. Thats always made it a little haphazard, especially in dungeons where there are just too many foes to focus on counterspelling. Also, frankly, its a little inglorious that your characters grand achievement during a battle was waving your arms each time your opposing spellcaster did. But it would be awfully impressive if the AI on spellcaster NPCs / monsters was altered a bit, so they did focus on counterspelling enemy mages, sometimes. It would certainly start making me worry if the AI started reacting by counterspelling (not dispelling), and definitely provide a new challenge to think through. Thoughtful AI for monstrous and NPC casters can do a lot, too.
Summoning. Duration on summoning is so awful here that its made most conjuration / summoning spells useless, and PotMs addition of so many feats to monsters and PCs has made those basic summons all woefully underpar. Unless you have graduated into a 15+ PC caster. I'd love to see any variation on the system off the current. Alternative summons, such as lower level elementals, quasits, imps, celestial beings, etc. in place of the basic furry animals that solely attack would be nice. One server I played allowed a wide assortment of alternative summons, if you possessed the right key item for the appropriate spell (tomes of infernal conjuration, bowls of water elemental summoning, old school items like that). Thats just a thought. What Ferro mentioned on Necromancers was a good one also... you don't see any necromancers in PotM calling up a zombie horde, or even doing the base necromantic summoning often, mostly because the creatures and duration is lacking. The death domains summon, the negative plane avatar, for instance, is a bloody joke.
Something else I saw in one game (not NWNs, nor D&D based) that made for an interesting challenge, was puzzles solved through application of various spells. Example, a barrier of ice that could only be weakened / removed through the application of any type of fire spell / effect. Admittedly, things of that nature often end up turning into little more than a "magical lockbox," where once you know the combination of spells needed are no longer remotely challenging. But randomization, and some creativity could do a lot for that. Again, just an idea. I'm fond of more puzzles / riddles being involved in adventuring and dungeoning.
One thing that ties into the spell components posts brought up. Focus items are often required for clerics and wizards. A cleric, more often than not, requires the presented holy symbol of his deity for many spells, and turn attempts. And a wizard flat out requires his spellbook to regain his spells. I do roleplay that my dwarven wizard carries a spellbook, which I drag out from time to time and emote "flips pages frantically and schemes deviously, studying spells." But its only a copy of Van Richtens. A system that enforced having a book out on rest, in order to regain spells, would be nice. Also devastate a wizard if he lost his spellbook... exactly as it should.
Also everything in Heretic's post, back toward the beginning, I really liked the sound of. Any spellcaster should do more than just go out and use their magic to crush foes. Enchanting, research, documentation, communion, desecration, consecration... all those kinds of things should really play a role in a spellcaster PC. A lot of that comes down to the individual, though, not the system. Can't script for everything.
Anyway, food for thought.