I suggest spell affinity be also gained for knowing additional spell trees. As in, knowing at least one spell in two or more combat spell trees different than the spell being cast. A buff to enchanters, basically, and to allow greater flexibility in spell choice for casters in general
BONUS DAMAGE:
So, in addition to getting bonus damage for knowing extra spells in the same spell tree, you also get it for additional spell trees you know, but at a higher CP cost. These would stack with damage gained from knowing extra spells of the same tree, but still max out at 5.
Possible options would be:
+1 damage per two total spell trees known, for a max of +4 damage before adding regular affinity
+1 damage per two extra spell trees known, for a max of +3 damage before adding regular affinity
+1 damage per two extra spell trees OR Deep Spellcraft/Sanctify Spell/Taint Spell, for a max of +4 damage, but at extra CP cost
+1 damage per three total spell trees OR Deep Spellcraft/Sanctify Spell/Taint Spell, for a max of +3 damage, but at extra CP cost
CAPSTONE:
Adjust capstone requirements from knowing all the spells in the spell tree, which is equivalent to having +5 affinity damage, to just having +5 affinity damage total. So you could replace knowing some spells in the same spell tree by knowing other spells trees. Though at a higher total CP cost. You'd still have to cast a T3 ranged spell.
SOAK:
Adjust soak gain so it's just +1 soak per two spells known in the spell tree, which would be the same max soak bonus, but allowing more flexibility.
Add a +1 restricted soak appropriate to the caster class alignment (Arcane/Holy/Unholy) per 3 or 4 total spell trees known, just as a counterpart to the soak gained by focusing on a specific spell tree.