Granted it could be considered a sci-fy "staple"...
As pointed out...the frequency is a bit less then fun for many. Also worth considering in regards to realism...
Being advanced enough to not only travel the stars, but wage war in them, why would a ship EVER consider simply sidling up to an enemy and attempt to board while simply praying the other doesn't blow up. The frequency with which it occurs via game mechanics makes it a VERY poor choice tactically for any but the most desperate, needy, or foolish. During such an action, it's worth considering, many steps would be taken to prevent such an occurrence in addition to taking any an all available steps to mitigate the effects of a self destruct.
Would be interesting, if possible, to see more options and stages for boarding actions to better reflect the choices and options one could employ.
Possible suggestions:
Options to allow for allocation of assault forces to better reflect the probable use of multi-pronged assaults on multiple critical ship components an key areas.
Ship module/systems for ships specializing in boarding actions that would mitigate the effects of a self destruct.
Varied types of marines allowing one to customize their assault via specialists
Allowing marines to garner experience, and through such a system, grow into various roles
Considering the above, ship boarding has the potential to become a interesting mechanic. Granted this is all with the complete understanding that it's ultimately up to Alex, and any helping him, as to whether or not such things would enhance or simply complicate matters. This is all just rough idea's in raw form, and I have no doubt already been considered in some form or another.