I was disappointed that Covenant was not a 3D presentation because I think that the viewing experience of Prometheus was enhanced by 3D.
When done 'properly', 3D visuals are entirely complementary to three-dimensional soundtracks (Dolby and DTS); and Prometheus is one of the best examples of this. Like a number of the respondents to this thread, I too cannot watch Prometheus in 2D because I know how terrific it looks in 3D; I fear the day when my 3D television gives up the ghost because I'm doomed to 2D viewing.
As I watched Covenant in the theatre, I kept thinking how great 'this' or 'that' scene would have been in 3D. At home, watching the Blu-ray, I still lament the decision to shoot 'flat'.
I often wonder if the lack of general interest in theatrical-3D is down to the absence of 'in your face' pop-out effects - a feature which misses the entire point of three-dimensional imagery.
On the 'consumer' front, I'm convinced that the half-resolution 'passive' system, coupled with the tendency of many viewers to sit too far from their TV's to actually perceive the 3D-effect, are the principal reasons for 3D's demise in the home-cinema arena. The expense of glasses for the 'active' system, and the mean-spiritedness of manufacturers to provide at least four-pairs, also contributed; but as the majority of consumers plumped for the 'cheaper' format, the end of consumer-3D was probably a foregone conclusion.
My opinion is that 3D, like LaserDisc, was wasted on the average consumer.