If you are on different planes of existence, there is nothing for your "Counterspell" action to target... to be targetable, the magic must be on the same plane as the counterspell to work... seems pretty simple to me...
Except, we already know that if something is stopped on one plane, it's stopped on all planes. If a dual natured person is stopped by a mana barrier, their meat body cannot continue on -- they're stopped. If an active focus is in someone's pocket on an elevator and the elevator passes through a mana barrier, either the barrier breaks or the focus is deactivated.
So, since all spells exist in both the physical and astral plane, since spells are inherently what we call dual natured, a projecting mage only has to stop the astral trace of the spell and that'll stop the physical spell as well. I don't see any conflict at all with a projecting mage counterspelling -- his counterspelling isn't crossing a planar boundary because the spell exists in both planes at once.
The problem is that the setting claims a less than 1% awakened population, but roughly 50-75% of runner teams tend to be awakened.
Let's presume that 80% of a team is awakened and that there are 10 people on the team. That's 8 awakened people. Presuming zero overall population growth over the next tumultuous 65 years, those 8 awakened people represent 0.00000013333333% of the total population. I'm not saying that the people in a Shadowrun team are the only awakened people in the world. No, I'm saying that runners, by definition, are special -- they're PC's!
Now, how many people have won any Nobel Prize? 829, so far. That's 0.00001381666667%, a very small percentage. I'm not comparing percentages directly, my point in asking this question is to now ask, how many of those Nobel winners personally know one or two (or more) other Nobel winners, or at least consider another winner a contact? People who are in rare categories tend to know other people in that rare category, especially in this uber networked time when it's so easy to just pick up your Google Droid and give someone a ring on their Skype account or something.