Ah, you're a person that needs the end of a prequel to link directly to the start of the original movie. Ok, but that doesn't always have to be the case does it?
Not all prequels follow that route, especially those that were planned as multiple movies from the start.
It didn't answer the question of whether or not the Engineers created the Alien, but did it need to? It doesn't take too much speculation to assume the Engineers either use the alien, or a distillation of it in the research into a weapon. The fact that something that is a subverted simpler version of the perfect organism shows up in the conclusion is a hint to where the Engineers experiments lead. By accident or design. Is the Deacon a watered down version of the ultimate weapon due the goo that created it being in essence the perfect organism, but only a droplet combined with two humans?
Did WY ever know about the alien? They only knew there was an alien signal emanating from a planet near one that they had previously explored and where their founder disappeared.
And Ripley? Really? Was she essential in the idea of prequel? Did you want a 15 year old Brett too? That's more of a George Lucas approach. I'd rather a prequel came from a more obtuse angle, than this fanwank name checking routine that serves no purpose other than knowing self-awareness. Which has no long term worth.