So I posted some ideas for making counterspelling more common a while back, but I saw the rules for dueling counters in Ultimate Magic, and I thought that would be a much better system to start with.
New rule:
You may attempt a dueling counter during normal combat, but you take a -10 to the counterspelling roll.
Additional modifiers
Wizard Specialists get a +2 to rolls to counter spells from their favored school, and a -2 to counter spells from their opposition schools.
Any class that gets bonus spells(sorcerer, oracles, etc) gets a +2 to counter a spell from their bonus spell list.
Any class with domain spells gets a +2 to counter spells from their domains.
Spell Focus and Greater Spell Focus both add a +1 to counter spells from that school.
New spell Counterspell
School: Abjuration
School abjuration; Level antipaladin 1, bard 1, cleric/oracle 1, druid 1, inquisitor 1, magus 1, paladin 1, sorcerer/wizard 1, summoner 1, witch 1; Domain magic 1
This spell works just like dispel magic, except it can only be used to counter other spells. You can attempt to counter with counter spell as a readied action or as a dueling counter. If you successfully counter a spell with counterspell, the target takes 2d6 damage per level of spell they were trying to cast(Will save for half damage).