He's just a much more refined boxer-puncher, now. It's been that way ever since the Marquez KO. But back to the topic, if we're speaking of rounds won in the second half than, yes, Mayweather is probably better. However, in terms of stamina in the second half, then I'd give it to Pacquiao based off his consistently high output and raising it the longer fights go on.
I remember reading an interesting assessment once about how it's a misconception that Floyd makes these genius adjustments and simply aims to fatigue the opponent and take control down the stretch because he is the fresher fighter, obviously I disagree that they thought Mayweather doesn't adjust because he does, he nullifies the opponent's biggest threat unless their biggest threat is being a deranged madman like Maidana or Castillo (first fights) and the Cotto fight he never really dealt with the educated jab but he started concealing the uppercut and sweeping around Miguel's high guard, as a good example.