Overall you should get most of the trophies just playing through the story. There are a few though that will take a little grinding.
Once you beat the last boss, you should be around level 30. Most likely you'll have these 2 left.
The fastest way to grind these is to keep replaying the last level, utilizing the Blue Magic speed boost. Regular blue magic works well here as well, the heavy attack having good AOE damage. You should be collecting items from the enemies, and potions from the boxes. Once you reach the boss's door, return to the tower, and do it again.
You should quickly reach level 50 doing this, but that won't actually give you enough points to buy all the abilities. Easiest thing to do without replaying the game is to make a save, buy all the abilities, and once the trophy appears reload your save.
The Blue Meanie trophy in Magus worth 33 pointsMax out the levels of all the Blue Magic skills. The Necromancer trophy in Magus worth 33 pointsMax out the levels of all the Red Magic skills. Another thing to keep in mind while grinding for the items is that you can turn them all into scrolls and in turn permanent stat increases. This makes the grinding faster as you will start to one shot the enemies.