Are the Space Jockey species the same as the Engineers?
There is a lot of controversy around this subject since Ridley Scott has explicitly stated that the Engineers introduced in Prometheus are the same race as the mysterious Space Jockey seen in Alien. As someone who saw the original Alien movie in the cinema when I was only 9 years old, I am one of those fans that disagrees with this revelation. It introduces a few plot holes, and I hope that another writer/director retcons this in a clever way. I also prefer to use the Spacey Jockey species name as revealed in the extended media as the Mala'kak.
Here is what I don't like about Ridley's decision and how I would fix it...
 

Scale
The scale of the Mala'kak to a human was one of the fascinating aspects and made this alien stand out. It is obviously much larger than a human. In comparison, the Engineers are much smaller and more comparable to a human in scale.
    
When the severed Engineer's head is revealed, we can see that not only the helmet, but also the head is similar in scale to a human head.
 
 
 
 
How to fix this plot hole and re-introduce the Mala'kak race 
Ever since the release of Prometheus , I have been pondering how I could fix this if I could. My solution to this is...

The Engineers are a bio-engineered slave species that are the workers of their Mala'kak masters.

The Mala'kak are the true bio-mechanical race and so far beyond our human understanding. Their natural languages could be quite musical, and this would explain the use of the flute like instruments used to interact with the Engineer ships.

The Engineer's ships are different to the Mala'kak Juggernauts as seen in Alien's Derelict. Although they both appear to be similar in design other than the command centres of each ship type. Mala'kak Juggernauts. The interiors are subtly different too. The Engineer ships appear more mechanical compared to the Mala'kak's more biological aesthetic.
          

If we also look at the pilot seat, the Engineer's seat doesn't include any hands where the arm-like structure is. While the Mala'kak has full arm and hand features. In addition to these details, the Engineer control centre pedestal has the cryogenic pods while the Mala'kak ship doesn't.

By incorporating these differences and there being two distinct races.

The story of Prometheus  as the plot for my Prometheus  theory: With the Mala'kak as Gods of the Alien Universe, a rogue Engineer is characterised by the mythical Prometheus . He steals the black goo from the Mala'kak and goes rogue with a clan of Engineers. This Prometheus  character comes from the planet that we see in Alien Covenant. He shares his knowledge and with a clan or cult of like-minded Engineers go to create their own slave race - Humanity. This is what we see during the introduction to the Prometheus  movie.
The Mala'kak discover this theft. They exile the Prometheus ' planet and peoples with a simple demand - Destroy your creation (Humanity). The exiled Engineers go to carry out this purge of humanity and prepare to weaponise the black goo, but it all goes terribly wrong, and they are unable to complete the mission.

During the event of Alien Covenant, we see David use the black goo on the exiled Engineer population. Look carefully at the population and they appear to be a simple people compared to what we saw of the Engineers from the Prometheus movie. They appear in awe of the return of the Engineer ship. If the Engineer population had been in exile, and they had some prophesy about the return to the fold of the greater Engineer society once the annihilation of humanity had been completed, that could explain this. Alas, David turned the tables on the exiled Engineers and wiped them out.

This theory could enhance the Alien Universe and bring back the mystery of the Mala'kak while cleaning up the plot hole highlighted by this theory.