Yes, it's clear that Prometheus ship was funded by Weyland himself so it could be a better ship than Nostromo but I can't believe that Prometheus, an older ship, uses digital and holographic technology while Nostromo uses analogic and 8-bit technology. Nowadays, for example, if I want to purchase a computer, the computer seller won't offer me a ZX Sinclair or an Amstrad if I want a cheap option. I think Scott and company should have been more careful with this (as Rogue One did)... I didn't say that Nostromo should be a better ship than Prometheus, I said that technology and atmosphere in general (costumes, scenery inside the ship, etc) should have been respectful with what we have seen in "Alien"; if not, it's not much credible.Prometheus was the state-of-the-art company flagship; Nostromo was a dilapidated tug. (Not sure where you get that Covenant has the same structure as Alien; the setup is similar, but it also owes something of a debt to Aliens, as well as going off in its own gothic direction.)
As for the films - enjoyed Prometheus. Enjoyed Covenant more. As much as I love Alien 3 and Resurrection, both prequels were better.
About Covenant, if I remember well, at the beginning of the film, the crew of the Covenant receives a transmission from an unknown planet and of course some of them want to go there but Daniels (in the same way as Ripley in "Alien") complains about the dangers. Needless to say, they go there and all die. If this was the first movie in the franchise, it's ok but after "Alien" and "Aliens" we all knew in the cinema how these "fantastic" ideas were going to end.
And I would add about the two films that there were one of the first "fan service" effects (and I hate it). Prometheus ended with Shaw and David head going to the Engineers planet, so the second part would be set in that planet with Noomi Rapace and Michael Fassbender as main actors. After watching "Prometheus" many people (or fans) complaint that this was not an "Alien" movie. So, ok, producers asked themselves: <<Do you want an Alien movie? Forget the script of "Prometheus II". Here it's, "Covenant">>. And what happened with Shaw and David? "No problem, we solve all these questions in a 5 minute short movie".