@Delernil
I think scouts are destroyed by ennemies when their antimatter tanks are depleted, then their capability "cloak" - that make them invisible - stops.
Without cloak, both covenant and USNC forces wouldn't be able to attack systematically at the hotspots of their ennemy empire, like Earth, Sanghelios, or whatever.

@TheJudge
Yes that the combination of covenants abilities and human abilities that enable the UNSC to fight back the prophets, and the flood.
Else "give ship" could be limited to covies with covies and to human with human.
In all cases, that ofter what miss me when I play with real humans. When map and fleets become too huge to be managed by one.

I everyone! I'm not quite familiar with SoaSE modding, so I don't know if the changes I propose are applyable. There is some improvements I mean for the gameplay and the roleplay:

GIVE SHIP:
As it's possible in any fleet, to use a ship from an other fleet (even the UNSC can use a covenant ship), it is possible for a faction to give or to exchange ships with an other faction.
I think it would be possible to add a low level research in diplomacy research tree, to unlock the capability of any ship to be moved into an allie fleet.
An other idea: the given ships would rebel themselves against our allie if thisone betray us.
Also maybe it would be possible to give ships only for a moment, and the ship come back in our fleet after a fixed time.

NO MORE EXPLORER:
The covenants attacked the Earth only one time, and didn't know at the time, it was the center of the Humanity. The UNSC always took care to avoid all its ships to slip space jump to the Earth during covenant attacks. But it's not possible in SoTP because of the unvincible exploration shuttles, then I think the exploration shuttle (or at least their invincible capability) should be removed.
It would make it possible to discover unknown worlds (like shield worlds and rings) late in the game too. That should be very role play !

COVENANT LOOK:

I noticed recently that for me, all your covenants ships were missing just one thing to be perfect: the good speculars. Existing ships in SoTP has a white, low shininess specular, whereas in Halo they has blue or red (copper like in reallity) high shininess specular.