In PvP Counter is strictly superior. Both moves have the same rate of energy gain while Counter deals more damage.
In PvE (raids/gym) Counter has 33% more DPS than Karate Chop while Karate Chop has roughly 41% more EPS than Counter. Despite this translating to using your charged move faster with Karate Chop, move sets with Counter have higher overall DPS.
By the numbers, Counter is the better attack. Having said that, I'd be pretty hard-pressed to get rid of Karate Chop purely due to legacy value.