I saw both players play in their prime, and I believe Baggio is the overall better player. Del Piero has definitely been far more influential for Juve, but in terms of ability and skill Baggio just shades it.
As for the argument about his performances in the CL, well, he never got a chance to prove himself in that competition, because we shipped him before he had an opportunity to do so. He also single handedly kept Brescia in Serie A, put in some mesmerizing performances for Bologna, and played extremely well in 2 world cups, 1990, and 1994. He was even better than DP @ the World Cup in 98 (when given the opportunity).