Very interesting about the Deacon. That would explain why it or something like it is in the mural in the orrery. (Was that the orrery?) I was under the impression the Deacon was a once in a lifetime combination the Engineers might never have encountered before, as they'd never had the chance encounter of human birthing a trilobite and therefore a Deacon. I got the feeling both creatures were more horrible accidents of genetics, side effects of misued bioweapons that David took home for Weyland, accidents of experimentation compounded onto the others that had befallen the Engineers thousands of years ago. Or maybe they have had a trilobite and/or a Deacon around before, maybe the process and chain of events doesn't work the way we think. It's all speculation.
I personally never had much problem with the Deacon. I think people might be more charitable had we seen it in full action.
I think they'll likely take even more risks on the next film, as this one did well and kickstarted the franchise again. From the perspective of a studio there's a lot to be said for risk management when you're trying to revive a dormant moneymaker - and when you've already taken major risks loosening its ties to the prior films, focusing in on an obscure element like the space jockey, playing with heady concepts and drastically reworking the original script, which was much more of an Alien homage package IMO. Thus, taking it easier with stuff like practical Fifield, etc. I think it'll just get more out there for the sequel.