As far as why the assymetrical-shaped 'juggernaut' craft seen in PROMETHEUS is essentially the same design (give or take a few details) as the long-derelict one seen in a different place in ALIEN (and ALIENS)...it could be that the version seen in PROMETHEUS was made around the *same* era to begin with (along with the other similar ships presumably underneath the other mounds too).
In fact, ALL the technology that the PROMETHEUS crew find on LV-223 could be roughly as old as the 'juggernaut' seen in ALIEN for all we know...considering we *don't know* how long that surviving 'Engineer' was kept functioning in 'stasis'. Judging by the many dessicated 'Engineer' bodies/'suits' that Millburn and Fifield come across, the whole complex is very, very old indeed - perhaps as old as the ALIEN 'derelict'. The fact that everything is still functioning is unsurprising...considering the supposedly technologically-advanced nature of the otherworldly 'Engineers' and the unknown, weirdly-exotic materials and designs they have come up with - remember, the 'warning' signal that the crew of ALIEN came across was still working fine after however many years the 'derelict' had been there. In addition, even the 'eggs' stored inside the hold of the 'derelict' still had a working layer of 'protection' over them, when Kane went to investigate.
(In fact, while it's still possible to just 'imagine' that the 'Space Jockey' seen in ALIEN was indeed the skeleton of a giant, 'snorkel-faced' alien creature of some sort, completely *separate* from the 'Engineer' race...if I had to compromise due to Ridley's 're-imagining' of Giger's original design, I guess I like the possibility that one of the 'Engineers' from the PROMETHEUS movie had managed to flee from the unknown 'outbreak' in one of the 'juggernauts' at the time, but was 'infected' beforehand...and consequently crashed on the planetoid seen in ALIEN soon after!
)
However, even if the ships in ALIEN and PROMETHEUS were made in *different* eras to each other, I still like to think that the main reason that there are only minimal design changes to the 'U' shape of the 'juggernauts'...is the fact that the overall design was so successful to begin with, and that there was no need for the 'Engineers' to change things drastically whatsoever. And given that the 'juggernauts' seem to be made of such exotic materials, these things were likely capable of lasting and working for many, many years - probably thousands, and perhaps millions...
Still, before PROMETHEUS came out, I recall imagining that it would perhaps be quite neat to see some other kind of 'Space Jockey' craft too, especially if there was some kind of 'fleet' shot in space of them all (which there wasn't, as it turned out
) For instance, I'd even imagined what a possible 'Mothership' might have looked like - a gigantic, non-spikey, 'Giger'-esque 'sea-urchin' shape which allowed for a group of 'Space Jockey' ships to emerge from an opening underneath. Oh, and by the way, I'd also imagined these 'U'-shaped ships to spin around in a slow, boomerang-like way as they flew forwards...
There's actually a bit of PROMETHEUS concept art which seems to show an alternative 'Engineer' ship design here -
http://www.avpgalaxy.net/wordpress/wp-content/uploads/2012/09/192815_326268787470185_1113144400_o.jpgHowever, it pales beside the strangeness of Giger's orginal assymetrical design, and only makes me wish that we'd seen another Giger-designed ship for the start of the movie, compared to the relatively standard-looking 'ufo' we ended up with.