The problem that I have with the Alien in Alien:Covenant stems more from it's usage rather than its design but its design is off as well.
My issue with the design is that it's just kind of bland. While one could argue its due to this being an early iteration, no cinematic Alien has been identical film to film meaning that at the end of the day, it's just kind of bland. The design is basically an exaggerated skinned human with a phallic head. It means nothing when you consider that there is no baseline.
What makes Alien designs good is the bio-mechanical look which also lends itself nicely to the insect nature of the creature. The Aliens of past films largely use this to help make the Alien stand out. The little bits of tubing or the carapace in places are all here to serve the design in catching the viewers eye. To the audience member who re-watches the film, you get a bit more out of the Alien the longer you look at it because of a richness of detail. But if I was to take off the head, back tubes, and tail, turn it red while placing it in something like the camp in Predators, you'd never know that was the Alien would you?
As I also said in the Skull thread, the Alien's skull is pretty much only here to be intimidating. It's presence is that of a screaming monster. However the Skull works on a number of levels and one of those being the "point of origin". For Ripley, "Kaine's son" is this nightmarish beast, it came out of one of her friends and is almost mockingly human despite being incapable of being reasoned with. It only looks human and further plays up the rape allegory that got her friends and the monster's paternal half killed. That and when the rape allegory occurs, it's further made uncomfortable by its human appearance which is warped by its otherworldly parentage. In Requiem while a nod to the Big Chap, the skull performs the same function. It's presence is almost mocking to Wolf as he's not only surprised this happened it's also using his people's strength against him and defiled a young warrior's honor to do it.
In Alien:Covenant its merely here to make the Alien look intimidating. While ALIENS dropped this for shooting reasons, it worked in its favor because it allowed it to play up the action while not forgetting its parasitic insect origins.