The question in Prometheus from Shaw to Holloway "Yeah, but who created them?"
That's the way out for the Engineers.
In general i'm fine with the Engineers as a design. They evoke qualities from some of Giger's work featuring humans. That ivory skin with the black eyes, it's featured in places in his art.
But what we could have gotten in it's place? A giant, sentient, wholly Alien creature? Man...
I've said it elsewhere. I always wanted to see David get DESTROYED by a proper Jockey. He awakens something, maybe with the intent of black goo-ing it so it will distract the human characters, thinking he's oh-so-smart and powerful, and the thing inside just crushes him like a can of soda with its mind. Doesn't yell, doesn't screech or howl, doesn't even raise an arm. Just crushes him like he's nothing.
Then it would look over at whatever human characters are present and stares for a beat. They're a small curiosity but ultimately of no interest to a being of its years and existence. Goes on with its business, leaving the humans stunned. Space Gods are busy.
That would be the tail end of the final act. The end of the movie would be very Lovecrafty. The universe just got a whole helluva lot bigger, and everything that went on in Prometheus and Covenant was just a side show compared to what's really out there.
Shit, if we need a proper Alien in a third prequel, we could even see the Jockey containing it in someway.