There are many interesting approaches to magic across the CRPG and JRPG spectrum. One of my favorites is the one seen in Betrayal in Krondor and Betrayal in Antara; it's very creative and innovative. I also found a game called The Four Crystals of Trazere that had an interesting system based on alchemy. Of course several of the Ultima games experimented with different systems, as did Final Fantasy. Some of them require you to find or buy reagents to cast spells, which I always thought was promising--though of course it's easy to just get tedious.

One thing I'm noticing in Company of Heroes is the rich interaction you have with the environment. It'd be neat if CRPGs could go that route; I've always longed for more sophisticated tactics that would take into consideration the terrain, cover, morale, etc. In particular, I'd like to have the opportunity to prepare a battleground or get serious with ambush tactics. Some games have made the attempt, but nothing like what I've seen in the RTS genre. I'm not saying they should borrow wholesale; but some of it could surely be adapted.

In any case, I've maintained that the magic system in most RPGs is roughly the equivalent of artillery in war games. I've seldom seen the sort of creativity with magic you have in the tabletop game or in the text adventure Enchanter (or Zork, for that matter). In my opinion, playing around with magic should be loads of fun, yet few CRPGs have really done anything truly interesting with it.