I'd wait until you've flushed out the old fluid to rule out air, water, or just old ass fluid being the cause. Otherwise, if you've got relatively new fluid in the lines and are confident the system is properly bled of air - if under any circumstances your brake pedal ever goes all the way to the floor (most likely in hot temps.) then it's almost certainly the MC unless it's leaking fluid somewhere (level would have changed on MC reservoir).
Just having a low or squishy brake pedal isn't necessarily a sign of a problem (better safe than sorry though) depending on the car. My low (compared with some cars) brake pedal didn't change with new pads but changing the fluid made it much firmer and, as of yet, has prevented the pedal from traveling to the floor in hot temps. However, I wouldn't be surprised if I eventually have to get a new MC since the fluid hadn't been changed on a reg. basis by previous owners.