So many ideas
I can just say, that the seraphim are WAY more than just the "kill everybody" you get confronted with in the FA-Campaign.
The true seraphim are peaceful and don't ever fight, they have a strong empathy to all living creatures (The Way). So basically they feel everything and thus can't kill or do harm.
However, there are so called Warriors who intentionally break with the Way, so they get rid of all empathy and turn into mindless killing machines. These are the seraphim you meet in the campaign (with one exception).
These Warriors are under the commando of a War Leader, who is still with the way and just plans the fighting and keeps the Warriors together and under control.
In one of the last FA-Missions you meet the War Leader who invaded earth, but you don't get to kill him.
So there are more options for a story than just a "kill all"-aspect.
The seraphim that got annihilated by the Humans on Seraphim II right before the vanilla campaign were special.
They were outcasts from the "real" seraphim, as they wanted to stay with the Way while being able to fight.
So, at least for me, a story between the attack on Seraphim II and FA, or maybe even into FA would be cool.
The protagonist could be some seraphim commander, who survived the massacre on Seraphim II and swore to revenge his people - he is with the Way and felt ALL of their pain.
So he tries to rebuild an Army with some other commanders, but they don't have a War Leader so one after another everyone of them goes rampage - they could even fight each other.
Throughout some missions you capture colonies fast - since you don't want to give anybody time to send signal that the seraphim aren't as dead as everybody thinks them to be.
Maybe you ally with some Aeon who help you out, fight some Aeon who think you are fake, fighting lone cybran that lost contact - there are lots of options.
You could even start the QAI-Hacking process, maybe by capturing modules of QAI.
But the internal conflict caused by the lack of a true leader dooms your revenge plans.
Right when all hope seems lost, you encounter some of the "true" seraphim.
Maybe you save him from something or you just get found by him - empathy and all that shit.
You tell your story and he brings you to a War Leader.
With your knowledge of the human technology and the hack of QAI they finish the preperation to invade earth and in the end you help doing so.
That's how far I thought about it yet.
Maybe you could even continue after that, with the War Leader being shocked by the many lives taken - which he really was - and some of the Warriors that invaded earth go rampage and need to be stopped - not necessarily killed.
Here ends my wall of text though.
Maybe you get the idea.
I have some ideas for missions, but they are no coherent story yet and I first want to know what you guys think of the general idea.
In the end it's still speeds decision
I have the feeling the seraphim are a very interesting concept.