A note about bonus prestige. Its calculated as a 'reward' for what you do during the mission ie destroying ships etc. Its also weighted by the total BPV ratio of opposing sides. This means, if you draft a friemd into a mission, and only have 1 AI opponent, you've probably got roughly a 2 to 1 advantage, and therefore, will only get half the bonus prestige. Here is a run down of the calculation.
For every enemy ship ship you get:
Internal Hits: 10% of BPV
Forcing to Disengage: 25% of BPV
Destroying it: 100% of BPV
Capturing it: 150% of BPV
This total is then multiplied by the fleet strength ratio calculated as follows:
Total Enemy BPV/ Total Allied BPV.
The more you are outnumbered, the more bonus prestige you get. Even just damaging several ships if you are heavily outnumbered can generate quite a lot of prestige. It can also be seen that where the opposite is true, ie. where you heavily outnumber your opponent, you're prestige is going to be reduced.
For allied ships, a negative modifier is applied. That is, you loose prestige for taking damage, being destroyed, again according to the above calculation. For allied ships other than your own, this modifier is halved, however, so you don't loose as much. Again, this figure is further modified by the fleet strength ratio, in this case it is calculated as:
Total Allied BPV/Total Enemy BPV
For example:
3 Allied Ships: Total BPV = 300 (say 100 each)
1 Enemy Ship: Total BPV = 100
In mission, you destroy your opponent but two of your ships take damage.
Bonus prestige calculation:
100% of 100 * 100/300 - (10% of 100 + 10% of 100) * 300/100 = 100 * 0.33 - 20 * 3 = 33 - 60 = -27.
In this example, whilst you won mission, you lost -27 points in bonus prestige. Why? Because you outnumbered your opponent 3 to 1, yet still two of your ships were damaged. Conversely, you can loose a mission against superior odds, but still rack up quite a lot of prestige if you managed to damage or destroy a few ships before disengaging for instance. Imagine a daring destroyer captain harrasing an enemy fleet taking pot shots and damaging a few ships before getting killed.
As a last note, the bonus added for damaging/destroying enemy ships is multiplied by 5 if your enemy is a human player. The negative modifer is not mulitpled by 5, so no need to worry there.