Ok, my thoughts:
Capping of capital ships and stations should definetely be a real possibility.
We should be able to get a group of marines onboard a station/cap ship after beating down the shields and doing, say, 70% damage to the hull, and then teleport them inside where they take a certain amount of time to attempt to capture the station.
Meanwhile, outside, the station calls in the big guns, and a large M3 fighter group or 1 or 2 M6s jumps in to take you on, and potentially reclaim or destroy the station/cap ship if it should happen to capitulate. - The boarding party will take some basic equipment. Maybe a couple of 125Mw shields and some disposable ECells to get the shields partially up immediately.
The boarding party maths should operate like this:
Argon are plain. They have to direct bonuses or drops in attack or defence.
Boron seem peaceful, but that would make unwary invaders weaker by a small amount, this would be teladi. They would also have one major advantage though... they live underwater, meaning that all invaders have to wear big and heavy oxygen tanks which, when hit, explode. So that all non-Boron attackers have a major HP drop. - conversely the opposite is true, any Boron invaders have to have their equivalent "water supply".
Paranid, are usually good tacticians and, according to argonopedia, are very strong, so should get bonuses to chances to win, and hit point boosts. The weaknesses they have, are they can't deal well with the cold (more likely to fail in worse damaged ships) as well as being bigger (and so easier to hit). They are also the most tactical, and therefore take longest to take over a ship. In defence, they should be very tactical, and therefore slow the enemy down most.
Split, are recklessly aggressive and are fairly strong. So they should stand a good chance of capping the ship, but also destroy non-essential equipment on board in the process. They would cap the fastest. - But they would be horrible at defence as they arent tactical, and they are too aggressive. So they would be overcame easiest.
The teladi, are, well, greedy, they had somewhat armoured plates, and are small. So thats HP boosts. They can change colour, so that means they can often take the enemy by surprise, so that gives them the first shots. They move well in water (though still need an air supply), so have boosts against the Boron defenders. The drawbacks of the teladi is that they stop moving when terrified: a split or paranid could terrify them and then crush them like worms, even some more aggressive looking argons and borons could do that. They arent particularly strong or aggressive so maybe attack worse, and as they are greedy, they could strip some of the nice addons (Any component worth more than say, 50,000).
In defence, they would be roughly the same as they are in attack.
Xenon have less HP than anyone else, but are faster, and more accurate with their weapons. - They negate all atmospheric effects: boron ships are just like all other ships.
Khaak, should be very very fast, fairly well co-ordinated, not so hot at the killing, are plentiful (3vs1 type outnumbering) but have only a few "critical members", who are responsible for the whole operation, kill one of them, and their defence or attack fails.
Elite teams: A mix of all friendly races who have boosted stats and some nice equipment that helps nullify all drawbacks (like a smaller air supply or thermal suits to help warm the paranid.)
This should all be done mathematically, while you attack the incoming defence ships.
The AI would obviously need to have access to these types of things as well.