OK. So the Shivans have been around 8000 years. As far as we know (and I _strongly_ believe this was [V]'s intention) they have been using at least 1 ship class for that entire time (The Lucifer). Now, that ship class has (presumably) had beams (or extremely beam like structures that are rendered exactly as beams in the intro cutscene for FS2) for all of those 8000 years. So the question is - why didn't the Shivan ships have beams in the great war?
The way I see it, there are two possible reasons:
1) They had beam equipped ships but, for whatever reason, chose not to use them in the Great War.
2) They developed/fit them to their ships, much as the GTVA did, in the 32 years between FS1 and FS2
Now, the problem is, there are logical problems wth both those ideas. For the first part, it's ridiculous to go to war with anyone using less than your best weapons, no matter what your aim is (ie. whether you're a cosmic destroyer, a galactic immune system, or just an angry, xenophobic alien bug). Beam equipped cruisers would have ripped through GTA/PVN capital ships of any stripe (Hell, Liliths can still rip through GTVA caps, if you get them in the right spots). So that doesn't seem logical.
The other possibility, that they developed (from original yellow Lucy planet killing specs down to standard red anti cap beams)and equipped them in 32 years faces the same problems as the first one (ie. they've had them for 8000 years (on the lucy) but only felt the need to equip them now?) as well as a few of its own. The cain, for example, is vastly more powerful than before, and thus is presumably generating much more power. Why was it generating all this power before beams? Or did the Shivans replace the reactor (the heart of any ship) as well, rather than just building a new, beam optimised ship (which would probably have been easier, given the amount of rewiring (or whatever) you'd probably need to do to to convert plasma turrets to beams.
Put simply, I can't think up a good, solid reason, as to why, in the GTVAs mind, there were no beam equipped Shivan ships (other than the Lucifer) in the Great War. I realize, of course, why there were in a real world sense (That FS1's engine couldn't support them, and FS2s could (probably at least partially as little more than a slightly gimmicky, but still cool, selling point)). For the record, I'm doing up some campaign backstory and I always like to write that sort of stuff from the GTVA's perspective, mistakes and misconceptions included. But this one has me stumped.