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:
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 !
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.