As far as I am aware, these are all of the negatives of Magic users:
1. Spells don't scale with weapon damage, meaning they will get outpaced @ 40 Int / 10 Pyro vs 40 Fin / 10 Warfare
2. AoEs have friendly fire, whereas Warfare ones do not
3. You need to match up weapon magic type with the combat ability skill line that you've chosen to put points into. In other words, if you get a really good Air wand on your Geo/Pyro, tough luck.
4. Enemies have resistances to magic attacks, but none to physical attacks. While enemies are capable of being weak to certain types of magic, this seems to be uncommon. Even if it were not, this merely introduces inconsistency to combat, and that's not something positive magic user's favor.
5. No Weapon skill line affects staff or spell damage. Whereas a Ranger can go 10 Warfare / 10 Ranged, or a Rogue can go 10 Warfare / 10 Scoundrel, or a Warrior can go 10 Warfare / 10 Two-Handed, etc., each getting more damage out of every point towards every skill they have, a magic user has only the 10 points in single magic skill tree for a single set of skills.
Any others?
Any explicit pros to magic users?