I can't argue specifically why the top one should be 12th and not 9th. It just seems like too much, too soon. 3rd and 9th is definitely out, at least in my book. 5d4 (Burning Hands) is a lot of damage for a 3rd-level caster to be dishing out. So maybe go with 6th and 9th.
About the 'greater skill level', I see what you mean, but at the same time, you should recognize that increasing caster level only helps the character's top-end spells. It's kind of silly to think that a 10th level character could have invested two feats solely for improving fire magic and get no benefit when he casts a fireball.
About the 'greater skill level', I see what you mean, but at the same time, you should recognize that increasing caster level only helps the character's top-end spells. It's kind of silly to think that a 10th level character could have invested two feats solely for improving fire magic and get no benefit when he casts a fireball.