Number-crunching time!
DPS
Pulse Laser: 303
Heavy Blaster: 500
Autopulse Laser: 1250 (250)
Without Expanded Magazines, Autopulse Laser has 20 shots, enough for two seconds of sustained fire. Expanded Magazines raises capacity to 30 shots, for three seconds.
Assuming no Expanded Magazines and constant firing of weapons without interruption...
AutoPulse Laser vs. (medium) Pulse Laser
2500 + 250x = 606 + 303x
53x = 1894
x = 35.7
AutoPulse Laser vs. Heavy Blaster
2500 + 250x = 1000 + 500x
250x = 1500
x = 6
It takes almost 36 seconds before Pulse Laser catches up to AutoPulse Laser, but only six seconds before Heavy Blaster catches up to AutoPulse Laser. Admittedly, Heavy Blaster generates much flux, and vent spamming (and giving up shields in the process) might be necessary to get full DPS out of blasters. With Expanded Magazines, the time it takes for medium weapons to catch up is 50% longer. For example, Heavy Blaster needs nine seconds instead of six to catch up with Autopulse Laser with Expanded Magazines. Pulse Laser needs more than 53 seconds to catch up.
Remember that Pulse Laser received a larger DPS raise than either Heavy Blaster or Autopulse Laser. Even that is not enough to overshadow the best weapons that received a lesser bonus.
The reasons to take Autopulse Laser over medium weapons have always been flux efficiency, extra range, and/or a quick burst of 2000 or so damage that can finish off a ship right now. If you think you need more DPS over a longer period, you are better off with Heavy Blasters or possibly Plasma Cannon since the latter cannot be blocked by missiles now.