I'll have a go at a few...
1-why does Shaw rebuild David
Why wouldn't she? She's completely alone, and would benefit from both the physical and mental assistance of another person, even if it is a robot. At the very least she needs David to translate the Engineer language, and probably needs his help using some of their technology. Also, David saved her life in Prometheus, and was created specifically to serve humans. While she may have some reasons to not completely trust him, she has no reason to assume David would kill her.
2-the john Denver song-is she infected/an alien at this point and its david controlling her or is she greyed out due to not being in movie
3-never explained how he infected her and is she dead when he launches virus on planet?
No idea. That's not the story the movie is telling.
4-is the end of the movie leading to alien?
Leading there, sure. Slowly. Not a direct path.
5-David lands on the planet but then is trapped there? Its an entire planet so did the engineers not have ships or other technology?
The Engineers had many planets. Obviously some must be very high tech. Some, like LV-233 in Prometheus, had only a single site where a ship could be found. Others, like Earth, had no technology left behind at all; just biology. Either the planet David found is a planet with life forms but no advanced tech, or there is a cache of tech hidden somewhere on the planet that David couldn't find. Either explanation is completely consistent with what we've seen of the Engineers.
General question-the alien hive from aliens has not been used since. Has scott given an indication he doesn't approve.
It's still open to go either way. David created the eggs, eggs make facehuggers, facehuggers make xenomorphs. It's possible David would create life that couldn't reproduce without him, but also possible he planned the next phase. It's equally possible that David doesn't know for sure what will happen next and the hive/queen phase is an unexpected mutation. Remember, it's all an experiment to him.
We have this huge list of mediocore/bad sequels and it would seem so simple for the studio to step in and say lets get back to how 2 was made
Still truly shocking that movies made in 1979 and 1986 are far superior. I'm beginning to want a restored version of aliens like lucas did with star wars and am hoping that Scott retires.
You hate all the Aliens sequels and want more of what Lucas did to Star Wars? Words can't even describe my reaction. No, just no.
Also, to answer some of the earlier questions:
Its interstellar comms system is incapable of detecting a transmission that the comparatively tiny one in a suit can (a meaningless plot point that has no significance or is ever relied on again).
The suit was outside of some interference that was near the ship. It was put in to explain why the signal wasn't picked up earlier. Really easy to explain and never relied on again simply because it wasn't significant.
There's only a single landing craft for an entire colony of people -- even the Sulaco carried a spare for just a single platoon -- which instead of having its med bay easily accessible from the main entry point chooses to stick it down a long corridor where you'd never be able to fit a stretcher.
There may have been another landing craft in the colony ship, just not one that was remote control-able like on the Sulaco. Given that it's years earlier and not a military ship, I find this easy to accept. I also didn't see any architecture problems like you did. Probably won't get a chance to review until the DVD comes out.
The basic set up of the film has the crew so reluctant to return to cryosleep that with no no hurry to get anywhere they have to go down RIGHT NOW without even pausing to map the surface which would have shown them the massive dead city.
Why do you assume they had the ability to map the surface in such detail, or that it would look that way from above? The stone temple/city area we saw actually had a number of structures jutting up around it, so the open meadow/lake they landed in would probably look like the best landing area from most scanning techniques.
The David series was so upsetting that Weyland chose to make the Walter series in its likeness to facilitate a supposedly surprising switcheroo
David was a prototype. A very successful one, that clearly took a ton of effort to design. Using the same mold is an obvious choice; you would have to work harder to explain why they should change it.
Alien Covenant was not a perfect movie. No movie is, and this wasn't the best of the series by far. But I think a lot of folks are asking way to much out of it and don't give it the credit it's due. A lot of these complaints are nitpicking a lot of minor issues that don't come close to some of the errors in the "good" films of the series. Ditto for Prometheus.