My biggest complaint with Covanent is definitely the lack of protective suits when first walking out on to an alien planet... That has got to be the single most stupid thing in the film - sure the atmosphere might be breathable but they cannot have identified every possible source of danger from flora, pathogens and so on. Being a colonisation mission surely they should all be following the motto of "prevention is better than a cure" and wear a damn sealed environmental suit.
The Captain making the decision to go to the planet, that's totally fine and believable given 1. Nobody wanted to get back into those sleep pods after the accident, 2. It was a seven year trip compared to a couple of weeks and 3. The nearby planet looked better than the original one they intended to colonise.
And actually the rest of the film was pretty good, even with some questionable decisions - ie the Captain going down into the creepy egg chamber and following David's instructions after seeing him "talk" to the creature that mauled one of his crew... That was totally dumb. Even if not knowing what those eggs are, every creature you've seen so far has been a hostile monster so why the hell would you trust a lying synthetic and even go near it in the first place. And then David's scene holding his hands out to greet the baby alien... that was pretty cheesy.
And true, Daniels could have done with a little more screen time in my opinion - otherwise it was pretty much a David/Walter film with the rest of the cast as supporting actors.
And finally it seriously cannot be the case that this is the home planet and only planet where the Engineers live (I'm assuming there may be more cities on this planet though the black goo would have wiped out all animal life anyway). I find it pretty hard to believe that David has wiped them all out. Otherwise it trivialises the whole concept of the Engineers if one rogue creation of your unintended creations uses your own weapon/tool of creation against you and you have no way to protect yourself from it. That is pretty stupid.