Other aspects of the magic system also followed a logic that I could understand: Advanced spells required understanding of basic spells (to make a Fireball, you need to know how to create a fire, then shape it). Spells tire out the caster. And so on. It felt... un-arbitrary.
Today I still like the magic system... mostly. Over the years there have been a few issues that have caused problems for me as a GM and for my players.
One issue is that there are SO MANY spells. I don't retain the knowledge of what each spell does, how it can be used, etc. As a GM I don't want to consult books to look up things in the middle of a game, but I don't have a better resource for spells other than the Magic book. This effects PC and NPCs.
Players (especially those coming from other games where they needed to know far fewer spells) have a hard time knowing the details of a very large spell list. I've often had a player forget they have spell X, but then something comes up where they feel that spell could be put to some use. Then, I need to look up the details to make sure the spell works as we think it does.
For my part, I dread making NPC casters. I don't want to use the same spell list every time, but creating a new list of spells and trying to figure out what each do and what is a good strategy can be a huge pain. I've tried just creating the 5-6 combat spells I think that they will need, but often find that if they had the prerequisite spells, the encounter would have played out very differently.
Even when I know what a spell is "supposed" to do, players are going to find new and creative ways to
abuse utilize them. This is usually a good thing, but does require a lot of off the cuff rulings. I tend to try to keep with the intent of the spell more than anything else. Many times, I find after doing some research and further thinking that I would have ruled a different way, and have to make sure I convey that to my players so that they are not angry when things don't work as they did last time.
None of this makes me hate the default GURPS magic system, but it does make it a pain some times. I've been tempted to use something other than the default system, but since my current game is DF I've decided to stick to the RAW as much as I can. If I had more time, I'd probably make a (digital) "spell card" for each spell that a PC has with full details of the spell, which would probably address my biggest issues.
I'd love to hear other issues, concerns, and solutions others have.