With the Advanced Edition, you have a few more options.
Best case: the ship doesn't have a Medbay (usually the early sectors), in which case you just rampage through the ship. The only concern is to make sure that you don't beam into a room larger than your assault force (if you only have a 2-space transporter, don't beam into a four-space compartment, or else you'll get double-teamed by the crew; beam into a 2-space room and take them in groups).
If they have a clone bay, you can set up camp in that room and kill them as they come out (and slowly kill the bay inbetween clones). So functionally it gives you a timer to get everyone dead, but I haven't noticed a substantial increase in difficulty there
If they have a medbay, then you have to get a bit fancier - the math is fuzzy on whether maxed out Mantis/Rockman teams can kill fast enough to survive, but there are simpler ways.
- The obvious - kill the Medbay with weapons fire before boarding. You can then beam to Medbay and prevent them from repairing or healing while you kill them all.
1a. Fancier - beam over to weapons or shields while you shoot the Medbay. Same end result, except you can often get a free kill or two when the weapons hit the medbay while Bob is trying to heal/repair.
1b. Fancier yet - Mind Control can really mess with combat math, especially at higher levels. You can
Lock them out of the Medbay with Crystals. Pre-AE, you had to use a Crystal guy - beam him into the empty Medbay, lock it down, then kill it before they break in. Effective, but requires getting one of the rare crew.
Hacking. This is the gold standard of anti-Medbay tech, and there are so many ways to mess with it.
3a. Hack the Doors system. While the hack is active, you move freely, they're locked in. Hack, beam, kill em' all. (Or beam, then hack to stop them from leaving when they're wounded).
3b. Hack the Medbay, version 1. While the drone is powered, the doors are locked. Set up shop outside, kill em while they pound on the doors.
3c. Hack the Medbay, version 2. Send the drone early, then power it off. (This unlocks the doors). Board as usual, let em run to Medbay. When the room fills up (or you've got all their wounded inside) power the drone and fire the hack. Not only are the doors now locked, hacked Medbays damage the crew inside, which will most likely kill off the folks trying to heal. Meanwhile, the rest of the crew can't get inside, bang bang life is good. (Higher hacking levels help here - I had the stage 1 boss hack my Medbay and kill two Mantis from full health to dead; that's when I learned not to stage the second boarding team in Medbay anymore.)