Never played any of the Masters of Orion games, but the idea of space marines boarding other ships always sounded cool to me.  Even if they're not trying to capture a vessel, they could still deploy at strategic points on an enemy hull to destroy critical systems that might not be targetable by other weapons.

I've never played any of the MoOs.  I have played Malfador Machinations' Space Empires III, IV, and V.  All 3 involve ship design with components, and tactical ship combat, where ship damage is in terms of components knocked out.

All SE versions have Boarding Parties as one of the components you can research (and Security Stations as the anti-boarding defense, but I always considered that to be wasted space -- I prefer to defend against boarders by just winning the space fight).  Boarding "uses up" the component (destroys it, same as damage, which is repaired normally).  Only shieldless ships can be boarded (so you must lurk at max gun range and beat their shields down, then sprint past their guns).  Hence, SE-style boarding basically requires tactical ship combat, and isn't compatible with GC-style ship combat.

The primary benefits of shippery are:

1. Tech stealing.  Your shipyard components can analyze a ship for any techs you don't already have (which eats the ship).  In SE{3,4}, this gave 50% of the research cost for that tech level (so basically, you must steal 2 ships with that part).  In SE5, it gives 100% of the research cost, and you get the tech right away.
2. Colony nova.  SE had 3 planet types (rock, ice, gas), each of which is a separate colonization tech.  (Atmosphere is not an issue; you can colonize the wrong atmosphere, you just get a dome that cuts your colony size to 1/5 normal.)  Soon after your boarders penetrate into enemy systems, you steal one of each colonizer type you didn't start with, steal those techs, and your # of colonizable planets triples.  That gets ... craaaazy.
3. Upkeep war.  In SE3, I preferred to cripple huge fleets of enemy ships, but leave their hulks motionless all over the frontier systems.  The AIs must continue to pay upkeep on them.  Later, I send dung beetle ships (a boarder-shipyard, which can capture and scrap for $) to clear lanes to the warp points, and gradually cleanse all systems in contention.  (This actually doesn't turn a profit, darn -- a shipyard ship is so huge that its own upkeep is already equal to the salvage value of a light cruiser, so it basically has to salvage one per turn(!) just to break even.)

You could probably make a strong case that #1 and #2 are ba-roken, and shouldn't be in a game anyways But that's what made it fun!!  It really wouldn't work in a GalCivk setting ...

I actually like the idea of capturing ships.  I think the developers mentioned something about a chance to capture ships and maybe acquire tech if you win a battle, once the full combat mechanic is in.  I agree that both features (capture and tech advances) should be part of the combat system.