Another plausable theory to go along with the whole Nomad angle, and that of the different design and technological aspects of the two Shivan armadas encountered, is that the Shivans are simply extremely Tribal in nature...
...Basically, they just wander the Galaxy/Universe in totally seperate tribes, raiding Space-Faring civilisations to aquire resources and/or fuel for their respective Fleets, almost the exact opposite of the GTVA. This fits nicely with the different looking design and technology of the two armadas. The Lucifer Fleet could have simply been a smaller Nomad Fleet that happened upon the GTA & PVN, an inveritable plethora of resources to feed their fledgling fleet. How this Fleet survived for so long, good ol' Luci of course. This also explains the colour of Luci's Beams being different from that of the Nebular Armada's, and of course her Shileds; which could both be a product of a technological progression that was once unified, but at one time became seperated...
...Keeping that in mind, the Second Shivan Fleet encountered in the Nebula would have been simply a different, considerably more powerful and advanced Tribe, likely the dominant one in the Galaxy/Universe, hence the slightly different designs of their ships and the widespread use of Beam Technology. Sure, they didn't have those funky Cap-Shields so they couldn't really call themselves basically 'Invincible', but with a Fleet like that, who's gonna argue? No one, that's who...
...Yeah, so basically, i'm going with the old arguement that, while the two fleets were of the same Species, they were of two different groups/tribes, thus explaining why the technology wielded by them was in essence the same, and yet at the same time, vastly different...
Edit; ...Lupus Nebula...uh...what's...what's that?