The wizard and sorcerer in my group have just discovered the awesomeness of Counterspell (after it was done to them a few times muhahahaha). I allow them to use only their Int/Cha mods based upon the 'Abjurer is better' interpretation.
I have been very lenient in their timing of the spell, but it is getting to the point where they want to wait for the results of the spell and then decide to Counterspell or not. I do not like this, and have instituted an Arcana check to identify the spell as it is getting cast; then they make their decision to Counterspell or not based upon that identification. So, in this instance, your proficiency in the Arcana skill is indeed taken into account and does have a factor in the outcome... just not in the actual Dispel/Counter roll.
I have been very lenient in their timing of the spell, but it is getting to the point where they want to wait for the results of the spell and then decide to Counterspell or not. I do not like this, and have instituted an Arcana check to identify the spell as it is getting cast; then they make their decision to Counterspell or not based upon that identification. So, in this instance, your proficiency in the Arcana skill is indeed taken into account and does have a factor in the outcome... just not in the actual Dispel/Counter roll.