Boarding also has the problem that you are risking your crew, which is hard to get by, and you are investing points into two, otherwise useless, systems (Teleporter and medbay).
On the other hand, I've found that countering the enemy medbay in time is a the key to win. If you can't take it out with weapons, have your two mantis boarders follow the escapee to the medbay. Two mantises can outdamage even a mark 2 medbay on a single target. Only works if you have other boarders to keep the rest of the crew busy, of course