Sitting aisle-aisle on a 3-3 configuration actually leaves more opportunties in the row for couples to sit together, not fewer. If it's A-B-C /D-E-F, choosing C and D leaves A-B and E-F. Choosing B-C leaves room for only one pair, in either D-E or E-F, but not both.

That does mean the the couple won't get and aisle-middle combo, but they might not have otherwise anyway if, in my latter example, somebody else comes along and grabs D. You simply can't predict every combination and every preference of the remaining passengers when you pick your own seat. For that matter, aisle-aisle couples are choosing to each sit next to a (gasp!) stranger in order to have two aisles--if they picked aisle-middle only one of them would be exposed to stranger's cooties.

Bottom line: as somebody said, it's first come-first-served, within reason. I normally fly solo and take sitting beside strangers totally in my stride. When I do fly with my travelling companion, we both like to sit aisle-aisle and we barely communicate with each other en route. It's really no different than having two unaffiliated people choosing those two seats becasue they were available at seat-select time.