Surprisingly I enjoyed this much more than Prometheus (Spoilers)
It's far from perfect, probably coming in at around the Alien: Resurrection level of enjoyment but it was vastly superior to Prometheus in its execution and delivery of a story.
Flaws I'd have to point out are that the Engineer world seems like a very friendly place compared to what we saw in Prometheus on that moon base.
As they have a large docking station in the centre of one of their cities they must have more ships out there doing whatever it is they are doing and so expect some sort of revenge from them in the future. How far do they go when they're off world and for how long?
They don't seem to have evolved at all since they birthed life on Earth 4 billion years ago (Or whatever).
James Franco's character seemed utterly pointless. Did he get a cameo because he's a fan of the franchise or what?
If David engineered the pods with Facehuggers in them, how did that ship with them as cargo end up being fossilised on LV 426?
If the Prometheus spent 2 years, 4 months, 18 days getting to its destination and was apparently lost it would take the same to get to their location to verify and same amount to head back to Earth to state that information. That's 7 years and a month in total waiting for an investigatory ship's return and yet this film was set ten years after Prometheus (December 5th 2104 to be precise, as compared to Prometheus' December 25th 2093 - January 1st 2094). David posing as Walter leaves a message at the end of the movie which states that if the message reaches the network is should be heard on Earth in 1.36 years. Supposing the message can somehow travel at the same speed as the ship (Faster that light) that means 8 years and 5 months have passed if an investigative ship was immediately sent out when Prometheus didn't arrive back on Earth on time. This puts the Covenant ship as having set of for 1 year and 7 months prior to the events of the movie. Placing "Paradise" closer to Earth than LV 223. Why didn't they recognise the Juggernaut ship?